So obviously I shouldn't make game decisions late at night after starting at code too much. Making the ship upgrades cost 100 Ship Structural Units per level meant a ridiculous amount of materials would be spent at higher levels just for the ability to add another module onto the ship.
So the way I've got it setup now is that it takes 10 SSUs to go to the next level, but if you're going up at new base level (i.e. 1.9 to 2.0) then it takes 30 SSUs. This takes into account that the new base levels allow you to also add another Engine or Command module.
I'm going to do the same thing for how much time it takes to upgrade ships also. There will be a built in 1 hour to take into account moving the ship in and out of the shipyard, then it will take about an hour for an upgrade that doesn't increase the base level, and three hours for one that does.
So going from 0.1 to 0.2 will take about two hours. Going from 0.9 to 1.0 will take about four hours. There will likely be skills for personnel at a colony that can modify this down a bit, so a colony that is more experienced at upgrading can get you in and out faster. I may also have it so a colony can specialize in Building or Upgrading so that you're faster doing one over the other.