I'm looking at running a game surrounding a sort of fringe Rogue Squadron, not unlike Wraith Squadron. Players would have their own custom starfighters, rather than all being assigned a standard model.

I had an idea that I could make 3 or so varied, but balanced stat blocks, and let them create their own shape and design around a stat block, and then get to do some after market upgrades. The basic models would probably follow the basic starfighter stereotypes: agile and fast but not heavy hitting (A-wing), slow but tough and packing a huge punch (Y-wing), and something intermediate (X-wing).

Does anyone have any methods for making comparable but balanced fighter designs? If not, would anyone be up for helping me make a trio of diverse but balanced ships?

Frankly, designing your own ships requires you to eye-ball it.

If all you have access to is the EotE core-rulebook, I'd say use the Z-95 Headhunter as your baseline and go from there.

For at least one take on a "fast but low firepower" starfighter, I did a write-up of the R-22 Spearhead over on the GSA. It's the EU predecessor of the A-Wing (article was written some time before the AoR Beta was announced). You could probably increase the Speed to 5 and not cause any real issues, though as written my take on the R-22 is a bit beefier than the A-Wing.