For some reason, Ascaron allows you enough upgrades to fully upgrade two aspects of your ship (Engine, Hull, Weapon) and some of the third. Why not just go ahead and hide away enough artifacts to upgrade everything?
Is there a mod that plants artifacts in various systems like that to gain the rest of the upgrades? Or even one that just fully upgrades your ship after having beaten the game, provided you found all the original artifacts?

You could search for a trainer that allows you to cheat and just add the last levels of the ship upgrades on whenever you like. Not sure which are good and bad but theres lots of them so one of them should be good to use, just make sure to virus scan any you download before trying them.

I'm aware of a trainer that will accomplish this from PiZZa, I think, and they're always reputable. Unfortunately, my AV programs love to trip over false positives, but I'm switching programs in a week anyway, I'm just waiting for it to arrive in post.