If you are using two GR-75's in a epic battle, first of all is this legal? Seems to me it is because they are only 2 epic points and you can have up to 5 epic points, and as far as I can tell they are not unique ship (but their titles are unique).

Second, does each ship retain its own personal set of damage decks, so you will have a total of 4 damage decks (not including the regular damage decks for small and large ships) consisting of ship 1 aft, ship 1 fore, ship 2 aft and ship 2 fore?

Yes you can have 2 of them in an epic squad

Yes, each ship would use its own separate damage deck.

I flew 2 transpirts in my first epic game. Very fun. I reccomend trying it. The synergies can be great. And yes they each have their own damage decks