I figured out how to fix this myself, go into the mod's workshop folder (steamapps\workshop\content\799600\3018217021\StarterFighters\enemies\Fighters). There will be 4 .rules files in there, all of which start with "fighter".

Open those files, and find "T5UfoSubfighter", and replace that with "UfoSubfighterT3". Rename the file "T5UfoSubfighter.ship.png" to "UfoSubfighterT3.ship.png". Repeat this for "T5SquadLaserSubs", replacing that with "T3SquadLaserSubs".

now its crashing within the main menu :/

Check main thread. I fixed the 2 issues above and will not rename or delete any more ships to avoid this issue.