Oh wow that's a really interesting bug.  I honestly haven't made it far enough in the game to make missiles myself, let alone see the AI make any.  It sounds like the AI is using the missiles as "super scouts".  Did you find a practical threshold to lower the missile speed to?

Try setting missiles to speed 64.  For testing, I made an "idiot nuke" unit that everyone could have at the beginning of the game.  I made it cost as much as a Scout so that everyone could get lots of testing.  I observed that speeds of 84 or higher would lock up the game, when the AI got around to trying to use them.  82 seemed safe, but as it was only a fission unit, engines at the end of the tech tree will introduce higher speeds and perhaps show the bug again.  I've currently got missiles with speed 64 and range 2.  That gives 128 fuel, enough to hit anywhere even on a Giant 256x128 map if you're careful.

I'm willing to credit you in the Changelog for having found this bug.  Do you want to be credited as "Esper" or something else?

As for the Democracy vs. "brutal police state" complaining, I have no idea.  Unless there's an "accidental paste" error somewhere from fumbling my keyboard, I didn't change any dialog lines for that.  I looked at the differences with a diff tool to make sure, and I found no dialog differences.  What faction were you?  Did you have a positive POLICE rating, say from building the Ascetic Virtues, or choosing Thought Control?  Maybe the game just looks at your stats and decides what kind of society you're closest to.

CHANGELOG
Changed from version 1.4 to 1.5:

- Missiles: playtester Esper discovered that missiles with a speed of 99 hang the game when the AI tries to use them.  Reduced speed to 64 and refueling range to 2.  This seems to prevent hangs and is still enough range to hit anywhere on a Giant 256x128 map.
- Planet Buster missile: changed cost to 300 minerals, equal to many Secret Projects.
- Conventional Missile: changed cost to 100 minerals, due to increased range, and to stop the AI from spamming them so easily.
- Tectonic Missile: changed cost to 150 minerals due to increased range.
- Fungal Missile: changed cost to 120 minerals due to increased range.
- Missiles: added as basic unit types so that they have accurate costs in the Datalinks.  The entries for Chassis types and Payloads are misleading because some odd formulas are used to calculate final cost.  Also, permanent unit types ensure that they don't disappear as unit workshop designs fill up.  I've had fission Planet Busters, gotten rid of them, discovered Quantum engines later in the game, but had no design slots free, so suddenly I didn't know how to make Planet Busters anymore.
- N-Space Compression: set growth=3 because Tectonic Missiles create new land and access to land, which can be colonized.

The attachment limit per post is 5, and I eventually ran out of room at the top of the thread.  Consequently, this becomes the new home of version 1.5.  It was downloaded 16 times before I moved it here.

Well my AAR effort folded pretty quickly.  The primary problem is I don't actually know how to play the Pirates with my new tech tree!  Lotta annoying stagnation occurred, shelling the Believers over and over again turn after turn.  The secondary problem is the narrative didn't have any meat on it.  I had initial ideas triggered by some items in the tech tree like Doctrine: Loyalty.  One might think of those tech tree entries as writing prompts or triggering events, excuses to tell a story.  But they didn't come often enough, for the number of turns spent, to develop into anything of substance.  It all felt very thin, and left me wondering, what would I actually like to see happening in a 4X TBS game, that isn't happening?  So at some point I might try again by completely making up gameplay, things that aren't actually happening and can't happen in SMAC.

Meanwhile I'm just learning how to play the Pirates properly.  I started out with a pure Conquer research focus, which is the default for that faction anyways.  This seems well advised because there are so many Conquer techs now, and it's important to keep up.  However there comes a point at which one really needs the Explore techs to keep people happy.  I didn't make a good transition on that.  Instead I just tried having "Doctor layabouts" while I continued with business as usual.  Typically I'd have size 6 bases with 2 Doctors.  I had enough food from all the kelp that this is doable, but my roleplay of "loathing the land" was counterproductive for actually destroying enemy cities on land.  Better luck next time.

But the Drones don't get that +2 Industry bonus either.  It's only +1 now.  They're also the only faction that gets an Industry bonus.  Yang's was taken away.  That said, all factions (except Morgan) can use the new Planned economy.  The Industry bonus is the same as before, but it also gives +1 Support, and the penalties are -1 Economy -1 Efficiency.  Easier to stomach, so it's a useful choice for anyone so inclined.

I played another Pirate game last night and did much better with the transition from Conquer to Explore.  However, I've repeatedly experienced an interesting research phenomenon compared to the unmodded game.  If you don't choose Discover at some point, you will never learn Information Networks.  This is a consequence of my "pure research" approach to the Discover track, at least trying to be as pure as the various lab facilities actually allow.  You can't count on getting Information Networks out of a pod, I popped tons of pods and never got it.  You can't count on the University or the Cybernetic Consciousness being willing to sell it to you.  You can steal it, if they're in the game, but what if you don't want to?  Or what if you do, but they're so far across the board that it's too tedious to push a foil probe team that far?  Well I guess at some point, a lack of research facilities becomes a real bottleneck, so you get more motivated to do something about it.  At midnight I just quit that game, lesson learned.

Probe teams BTW have nothing to do with Information Networks etc.  You get them from Planetary Networks, but the prereqs are Doctrine: Mobility and Doctrine: Flexibility (which is an E1 tech, no prereqs).  The idea is that probe teams are considered to be Conquer technologies.  If you think about it, an information network does not have to exist for something to be hacked.  What about units?  Mobility and Flexibiliy were chosen so that I could guarantee a Foil Probe Team was an appropriate thing to enable with Planetary Networks.  And yes, the AI does use them.  They will come all the way across an Enormous map just to bother your sea bases.  I've been building armored infantry chassis probe teams in my sea bases, defensive units that aren't expected to go anywhere.

Minus the planet penalty which I always found stupid.

I retained it for narrative flavor.  The idea that they think it's Eden, and not what it actually is, appeals to me.  It is reminiscent of the old Star Trek episode The Way to Eden.  Juicy ripe grenade fruits indeed!

The Cyborgs are overpowered now though that crippling growth
penalty was the only thing that kept them balanced.

I disagree.  You may not have noticed that their RESEARCH is only +1 now.  Zhakarov is the only "on steroids" research faction with a +2, and these are the only two bonus research factions in the game.  Hmm, steroids don't sound like the right drug, what do those lab rats take to keep working?  Gotta be more than coffee.  Besides, Roze surely monopolizes the coffee trade.

The only faction I'm wondering if it's really overpowered now, is the Spartans.  They seem to kick major booty.  I will be watching them.  I haven't actually fought them yet, as playtesting has tended to reveal "yet another thing that needs changing" before actually getting across an Enormous map to them.

As  far as the social engineering  changes. Free Market penalties are a bit extreme

In my mod they are less than the penalties of the original game.  And you get +1 EFFICIENCY, because let's face it, Free Markets are more efficient in some brutal sense of the term.

Power the Industry penalty is crippling.

Not as crippling as it was.  It's only -1 now.

I retained it for narrative flavor.  The idea that they think it's Eden, and not what it actually is, appeals to me.

By that logic they should get a plus to planet not a penalty. Its just the anti Christian bias again.

The only faction I'm wondering if it's really overpowered now, is the Spartans.

Spartans always do well because they're aggressive and they bring rovers. Its more that than anything else.
Drones always did poorly because their AI is passive. The cyborgs took forever to build for the AI but if left
alone were obnoxiously powerful. Its the Research paired with Effic.

In my mod they are less than the penalties of the original game.

Free market economics penalties in the base game were just stupid. Your mod makes it better but I think the penalties are still too much.
I just solved the problem of penalties by removing most of the penalties for everything.

Not as crippling as it was.  It's only -1 now

.
I never liked the industry penalty. The problem is Power is actually quite good.

Unfortunately I could not get this mod to work.

By that logic they should get a plus to planet not a penalty. Its just the anti Christian bias again.

Umm maybe you didn't watch that STTOS episode, but the ringleader died from eating poison fruit in the "garden of Eden".  Because, as Spock attests, this cult leader is actually insane.

The question is to what degree the Believers are completely delusional about what Planet actually is.  Narratively, the story doesn't actually talk about it all that much.  Maybe not at all?  I can't think of a single quote where Miriam rattles on about "we think it's Eden".  Of course the original SMAC opens with the passage from the Conclave Bible, but there's nothing about that reading which suggests the Believers take it literally.  All we really have is 1 line of text in the Faction description: "Believe Planet is their promised land."

Talking about Planet seems to be Deirdre's schtick.  Then in SMACX, the Usurpers get to fantasize about becoming gods.  I think the Believers' viewpoint on the Planet sentience is actually unknown and uncommented upon, other than that 1 line.

The Believers go on and on a lot about God really existing, "just behind the last theorem".  Zhakarov and Yang present the atheist points of view.  The Believers also get really worried about various "false gods" being elevated above humanity, whether nanorobots or self-aware colonies.

Then for the Universal Translator movie we get thrown a loop where there's something seemingly Biblical on a Monolith somewhere.  WTF?  Little too gratuitously X Files or Ancient Alien Astronaut theory for my tastes, mainly because it wasn't really set up to be intelligible.  I feel like someone just made a SP movie with a curve ball thrown in.  Narratively in terms of the entire story, it strikes me as pretty weak.

It might be an interesting exercise to write a more religiously themed story, as SMAC is being played.  I'm not sure if those occasional narrative "screens of text" can be modded or not, to put more meat in a narrative.  I'm not willing to do voice acting even if it could technically be done.  Writing is "cheap" and expensive enough in terms of doing a good job.  Voice acting, I think that's more appropriate for one's own intellectual property.  Frankly if I made my own 4X TBS I don't think I'd voice act it at first.  I think I'd make it an expansion pack and make people pay for it, either as an addon or crowd funded.

Spartans always do well because they're aggressive and they bring rovers. Its more that than anything else.

I took away their starting Rovers.  They have to research Doctrine: Mobility just like anyone else.  Basically the Spartans are now +2 Morale, that's it.  No bonuses, no penalties.  They do get their free prototyping as before.  Something seems to be a bit messed up with prototyping in general now though.  Maybe because I included basic unit designs?  Oh well, I'll investigate later.

I never liked the industry penalty. The problem is Power is actually quite good.

Social engineering choices are supposed to be tradeoffs, not just new free stuff.  I thought -2 Industry sucked hard, so I changed it to -1 Industry -1 Economy.  I general I find that all these -1 Economy penalties I put in lieu of other things, do end up hurting as they accumulate.  You start noticing you don't have enough money.

Unfortunately I could not get this mod to work.

I'm not sure what the problem would be?  You drop the .txt files on top of a plain SMACX installation.  I use the Good Old Games version myself.  If you are using something patched like Yitzi that also changes alphax.txt, then yes it's going to be completely hosed.  Install a clean vanilla SMACX in a different directory, then drop the .txt files on top of that.