I can't seem to find the ship upgrades, for awhile it was fine but now I'm on the goddess boss fight and my ship is way too weak to survive it, how do I upgrade or find the upgrades for my ship? 

All upgrade is unlocked by progressing the story.
You can craft upgrades at the bottom right area.
Some upgrades like shield have to be installed manually at the bottom left area.

can i ask how to find the maintenance kit ??