I had loads of scrap to spare ( at the end I just upgraded for redundancy since I didn't have enough energy to power everything. ) Weapons: Ion blaster Mk II, Small bomb, Fire beam and Burst laster Mk II.
Kinda felt weird, my weapons

, worked tho. Fighting the boss was not too hard, but I almost lost with 3 hp bars against the 3rd flagship's "super weapon", finally figured out one shot from death how to dodge it with cloak XD.
Oh yeah, you guys might be interested to know i had 3x automatic reloader for .... +45% atk speed? XD
I didn't use any repair station after first fight, didn't wanna risk it.