I played EV Nova religiously for a number of years a while back. I must've played through each plot string at least 3-4 times. At some point, I made guides for myself so I would know how to upgrade the ships to my specs each time.
I should also note that I didn't take advantage of glitches in the game that allow you to gain more than you should be able to get in these setups. I think it really only applies to the Unrelenting, but it's still worth mentioning. If you get your ship upgraded just how you like it right after you get it, any upgrade you get as part of a plot string is added on top of whatever you already have (even if you don't have the space for it).
Anyway, here are the guides I made a few years ago. Good times... kinda tempted to start up a new game now!