I've found an error in your ships.txt referring to the nonexistant "Mirage Light Fighter-.ship.png" instead of "Mirage Light Fighter.ship.png". This is causing crashes on FTL into some some systems.
Several ships.pngs int the mod are not in the text file. A number are duplicates with numbers in the name and no '.' before ship but some are just not present. There is also a "Suffren Class Cruiser.png" that is a duplicate of "Suffren Class Cruiser.ship.png".
Caterpillar.ship.png, f-1.ship.png, and "TTE Missile Orb.ship - copy.png" (which are among those not in the text file) use extraneous mods.
oip.ship.png and 'small pirate.ship.png' (also not in the text file) are not recognized by the game as valid ship files.