I assume the stoma and bubbles are no longer a problem. If so, I wouldn't worry about the squeaks unless it repeats. Then, you'll need to figure out what's causing it.
Regarding your humidity struggles. I'd advise you to use a large flat-bottomed water bowl and humidity holding substrate. I hear Reptichip works well. If that doesn't work, I'd close the remaining vents. Cover them with tape on the outside of the enclosure to test it. If it works, you can seal them with spray foam or silicone for a more permanent solution. You'll get sufficient ventilation around the doors. Adding a humid hide is also a great idea.