If you don't mind a bit of input, my totally unprofessional words follow:
1. It's no longer, "ITU, ITU, ITU". There are three different range-extension Hull Mods; they all come with some sort of nerf (depending on factors). Dedicated Targeting Core, for example, can be put on all Hull Sizes, but it costs turret speeds; ITU is cheaper OP-wise, but it comes with acceleration and turn nerfs; Advanced Targeting Core is installable on all Hull Sizes, but it comes with a significant speed nerf. I don't know whether these are all the right answers, in terms of effects / costs; expect some adjustments (and your feedback is welcome).
Why all these buffs, and why the specific effects? Simply put, range is the primary "god stat" of this game; it determines whether you can kite indefinitely or whether you can alpha enemies before they can even inflict Hard Flux on your shields. The nerfs reflect that.
I like this, having a cost/benefit to the range+hullmods is nice, so I think something like this is overall a pretty wholesome idea.
2. Expanded Magazines is useful for anything that wants high alpha; it boosts firing rates by 50%.
That's not what alpha means, and that's a really strong buff don't you think?
3. Missile Racks has been replaced with Heavy Missiles; it's a flat damage bonus, so that it's universally useful.
I would actually argue that you want to avoid universally good hullmods. After all, that's why you made 3 range+ hullmods, no?
Also, as far as coding goes, any modification to the damage of a missile only applies to the initial warhead. This means it will not have an effect on MIRVs, Sabot style weapons, or anything else that has different to-hit values based on stages. I had the same problem doing my own modding (not that I'm a pro or anything).
4-6 are solid based on your descriptions, though I caution you against making the flux shunt equivalents too powerful - it's very easy to make something like that objectively overpowered (Paragon, anyone?). Solar shielding buffs are :100: though I really want to like that hullmod but it doesn't really do much, and .8 definitely gave a buff to ARM that hasn't been addressed so if you dislike that I completely understand hitting that a few times with a hammer.
THIS IS ALL IGNORING THE MOST GLARING ISSUE: FLAT DAMAGE INCREASES AS A MECHANIC.
http://starsector.wikia.com/wiki/Locust_SRM_Launcher
7. Heavy Armor is actually worth buying for stuff that isn't the Onslaught now, and makes the Onslaught, Dominator and Enforcer fit their role better; it's also really good with Ion Shielding on the Hound and Cerebus.
Well this is just a shame to read! Pretty much any low tech ship benefits from heavy armor, due to the exponential nature of armor and the reduced weakness to mobility-sacrificing hullmods. I don't necessarily disagree with this modification, but are you sure you're not underselling the value of armor?
8. Augmented Engines has been replaced with Efficient Engines; reduced Fuel cost. Finally, a Hull Mod for those transports, if you don't mind the Sensor hit.
Given how hilarious and gimmicky nav3 is, I never use Augmented Engines anyway, heh.
9. ECM Package is a flat bonus, not a Hull Size bonus. It was too unattractive and cost too much to put it on big ships; instead, consider getting a leg up on your fleet's ECM rating by putting it on disposable Frigates or hardened Destroyers.
What you're describing is, as I understand, the entire reason it's locked to hull size. My only suggestion here is to inflate the cost for smaller ships so it kinda meets in the middle. Thematically I don't see anything wrong with electronic warfare frigates since realistically this is how thing's be, at least in my head (and in mass effect!), so this is just a personal hesitation, you do you.
10. Probably the most-controversial change; PD AI now gives a flat damage bonus to PD weapons against Missiles / Fighters and does not affect the AI of weapons. This was really necessary because, combined with ITU / Advanced Optics, it made Wolf swarms with Tac Lasers a little bit too much of a "right answer", imo, because they could clear missiles and fighter swarms, especially if backed up by an Enforcer or two. I may drop the OP cost a bit later on.
Eeeeeeeeh, was spamming wolves
really that good? I mean, doesn't sound like those guys would be able to fight anything bigger than other frigates...
I dunno what #11 means so no comment.
12. Flux Shunt, if you can ever find it, can be installed on any ship. It's expensive but it's quite effective with the other Hard Flux drains. Might adjust the OP cost later.
There was a glitch in a mod, I wanna say SRA but don't quote me on that, in .8, where you could get a "mini" flux shunt that was something like 15%. It was basically a return to the .7.2 perk, and you're suggesting 50%. This is a Bad Idea
tm
13. Salvage Rig is now installable on any ship, and effects post-battle loot. It's actually pretty attractive to have it on a few freighters, etc., if you're pretty sure they won't need the OPs for running away during Escape scenarios. In save-scum games, it's very attractive, but I can see it getting used in Iron Mode, too, to maximize loot.
Either buff the salvage rig itself or nerf the modular hullmod, else there's literally no reason to ever field a real salvage rig. Otherwise this opens up another style of play (nonbounty salvage combat) and I'm all for it, if slightly wary that it'll be too good.