Well, congrats on your first mod.
As far as feedback goes, I'll refrain from talking about balancing and such since you have enough experience to know about that and what people see as balanced differs.
What I can tell you though is that multiple artillery systems are likely to cause problems.
The main problem being that resetting the run or continuing (after a save and quit) removes all but one artillery weapon.
There's also the thing of one not being able to be turned off or upgraded but I assume you noticed that during testing.
Furthermore, I see you have disconnected rooms, not sure if those rooms can be accessed or not, but keep in mind that it does come with a problem.
And yes, I did notice the repair bomb as a way to repair the systems, the problem however are lanius boarders. Though rare, do exist. If those end up in there, they won't be able to be killed.
Which means the ship is in constant "danger" and you can't upgrade anymore for the remainder of the run or until an enemy ports them back.
Besides that, some minor graphical things like the glow around the ship and some awkward interior images (O2 for instance).
All and all, not a bad first mod. Keep up the good work !
Amateur modder and Let's player (with a substantial FTL and ItB LP featuring countless mods).
A list of all my mods can be found here