I know there's likely going to be some issues with balance, especially regarding the Prethoryn probably. I tried to follow certain rules when adjusting ship hull/armor values, which are as follows:

(Num possible slots means the number of slots the FE equivalent has that can fit x component. Exceptions include Starbases and Civilian ships.)

Prethoryn:
Hull = 250-750 more health than FE ship equivalent.
Armor = base + ((neutronium armor slot value * number of possible slots) + (previous value * 0.5))

EXD:
Hull = base + ((crystal forged plating slot value * number of possible slots) + (previous value * 0.5))

I think this resulted in too high numbers for the Prethoryn but too low numbers for the EXDs, though this doesn't account for their shields. For weapons, it was more try to make them 20-25% better in general than their non-special equivalent than any set formula. The only weapon I'm definitely irked by is the Large Matter Disintegrator for now, I think the max damage increase was too large..