i defeated him 3 in a row, i didn't go anywhere to repair. i probably should have though i was WAYYY too close for comfort, 4 hull and 3 crew out of 8 survived on his last super weapon thing.
my strategy for the engi ship is get the augment that allows you to recycle robot parts as soon as possible
then stack anti-ships and you're in the clear for victory. near the end i was bouncing around 600 scrap because i had nothing to spend it on. i had full battery.