
The Piercing Ranseur Beam, while it still takes 3 power compared to the standard variant, doesn't seem to pierce shields.

The Missile Defense Drone II's Title name overfill the box.

Both Overclocked variants of the Laser Repeater series (I and II) overfill the box.

[Insert redundant explanation here] (Reactive Healing Cluster Burst)

The Overclocked System Disruptor III overfills the box.
All Heavy Ion weapons and their augmented variants also clip the short name box shown in the cargo/store GUI)

Advanced Rebel Elite Cruiser cuts in-between the hull meter.

All engineering options overfill the event box when you have enough equipment to display. (To be honest, I have no idea how to fix this without making it look like a sore thumb.)
Also in my spare time while translating Arsenal+, I've made my own personal fixes for both Insurrection and Captain's Remix, Replacing the Lanius and Kestrel B's cloaking image with one that's more similar to the normal image, refining a glow issue with the Heavy Laser Drone I, displaying the Ship Module names when you unlock them at their faction's Homeworld event, and a new title screen (Insurrection Only) including the proper copyright text.
If you'd like to integrate my fixes onto your mod, PM me and I would more than happily offer them to you. (because my Mod's list currently looks worse than the Sega Genesis with all its modules stuck together.)
WARNING: FTL Captains Edition was not designed to be played with Advanced Edition disabled.
Also, are you going to address the AE toggle issue with Captain's Remix anytime soon?