I found a half dozen bugs, but I don't think you care at this stage, so I'll stick to broader thoughts:
I really like the new pace of things wearing down. Not only do I feel less annoyed by air cyclers, but it's also clear that different components are becoming an issue at a more even rate, as opposed to always going for the cyclers and coolant, and ignoring everything else. Best of all, it feels more like "maintenance" to me: something you can feel proud of staying on top of, or push off until your ship looks like a beat up mess. My favorite moment this time around was when roleplaying as a space redneck who ended up late on a delivery because he had to keep running back and forth fixing the warp nacelles, only for something else to go wrong when I tried to start them up again.
Stamina is in a weird place at this point. In the first few levels, it's an important element of strategy. You physically can't maintain a whole ship without overexerting at level 1, so you have to pick and choose which components are important, and having to pick up and drop four boxes in a row to get to a clogged air cycler can be a fatal mistake. Later on, your stamina bar gets more lax and time becomes the limiting factor to completing missions effectively. The biggest problem is that if you screw up and run out, your only option is to sit around for a minute and let it regen. I would suggest thinking about how important stamina is to this game, and either factoring it into game balance, or removing the system.
I think there's more you can do with repair missions as "levels" with existing pieces. Because they are optional and don't mess with the player's ship, you might want to look into using creative layouts as puzzles, or even tutorials for less used parts of the player's ships. Examples might be an extra fast zoob on a ship with enough boxes to coral it in with, a ship with a simple problem but a maze of cargo in the way, or a ship where the fuel tanks are pure residue and need draining.
In my experience, the most common case for a component giving off emotion bubbles was in the warp engines, right before warping. In that case, you can't tell what the bubble is referring to, kind of making it useless.