Well I finished game not so long ago and started to mod things in FTL (click to enlarge):
After some modding test, what things will work if you mod and what not:
* Amount of power in ship can be only altered by changing <maxPower amount ="60"/> - it's amount of power that ship starts with, basically if you will set it less then 25, the maximum amount you will be able to get is 25 through upgrades.
* You can set any amount of shields through maxPower in shields' settings. I had to change GUI a little in order for shields pictures to be in line.
* If you set maxPower more then 8 in engine settings, next level of engines will just have same effect as level 1 engines.
*Max level of oxygen can be set any, it will produce more and more, with level 8 o2 boost multiplier is 21x.
* Leveling medbay to level more then 3, will have same effect as with engines. Same goes for Teleporter.
* You can increase maximum level of cloaking device, but on level 4 graphics partially available for it and on level 5 no graphics shown at all.
* Weapons and Drones can be set to any maximum level you want.
* All subsystems, when go above level 3 start giving cloaking ability, but without button to activate it
* Regarding creation of new weapon - you can put any possible settings to it, that exist in other weapons
P.S. bas, thank you for awesome modding tool