I was wondering if anyone knew how to modify the appearance of the in game races ships to say give the Pilgrims' ships the appearance of the Cravers. Is this possible and if so isit also possible to say modify only certain classes of ships like to change only the Pilgrim's dreadnaught to the Cravers' model.

Yep. For the initial question, easiest answer is simply to use the "Create a race" thing from the game, but as for specific models, they're all listed under "Affinities". For changing the Pilgrim Dreadnaught to a Craver one you'd swap in "DreadnaughtRebel" for "DreadnaughtSwarm" for the model.

I walked through how to change the faction's ships in detail in the 3rd post of my custom faction guide thread. Hope this helps!