There's a lot of people who wonder why Gallaxhar bothered to put Susan in a different outfit before draining the Quantonium from her. Keep in mind that the outfit shrinks with her, which the one she was in before wouldn't have done. And seeing as he already expressed disgust with her form and the clothes she was wearing before wouldn't fit her anymore, he probably wanted to spare himself from the sight. As to answer the how, he probably had something else change her outfit.
The ship's computer, by way of a dozen robot arms of course. It even sounds female.
The spaceship is about to self-destruct. B.O.B comments cheerfully, "I'll see you guys tomorrow", and the joke is that he's an idiot. And he IS, but he's an indestructible idiot. After all that we've seen him go through so far, it's hardly a huge stretch that he'd survive the ship exploding. He's just forgotten they won't.
We've seen him crushed under a giant robot's foot. We've never seen him survive extreme heat or high speed pressure waves. An explosion may still kill him. You could make the same argument that Dr. Cockroach would survive, because the entire point of becoming a cockroach was to have the survivability of cockroaches (which are commonly believed to be able to survive a nuclear war. They can't, but this movie's logic would say that they can, and thus Dr. Cockroach would also).
The theme song of the series is a case of Fridge Brilliance due to the fact that unlike the film the idea is that the nature of the title is now more about the rivalry between Team Monster and Team Alien.
There are some subtle hints in the film and sequel TV series that Dr. Cockroach has a crush on Susan. He was a human before becoming Cockroach, so his implied feelings for Susan would be understandable.
According to Dr. Cockroach and Link, the Invisible Man's body had been in that same chair in the room ever since he died, rotting away. Good thing he's invisible.
But can't they smell him?
Dr. Cockroach is a cockroach, and therefore probably doesn't mind smells — he eats garbage, after all. Link is aquatic, and fish stink too, so he might not mind either. BOB is an idiot, and may not even have olfactory senses.
How did the people at the facility manage to undress Susan and re-dress her while she was unconscious? Changing an unconscious person's clothes is difficult at best, and when the person in question is that big, it would be a truly, well, enormous challenge.
One way to solve this challenge would be to cut her out of her wedding dress to undress her, then drape cloth around her and sew the hemlines, etc, onto her. Essentially make the clothing around her. At that size difference, this would be much easier than trying to move pre-sewn clothing around, let alone dress her. The real question is why would they go to that much trouble? It would be much easier to leave her in her wedding dress, leave the clothes in a pile next to her bed, and when she wakes up say "Please change into the clothes provided and place your soiled clothes into the receptacle." If they really needed to get her out of the dress right away (say they need to study it for the Phlebtonium it may have absorbed), it would be much easier to dress her in a hospital gown and made her change when she got up. That's kinda the point of hospital gowns.
How long was Susan knocked out by the stuff in the oversized needle? Long enough to move her from Modesto, obviously, but how long after that? Long enough for them to make/obtain clothes for a 49-foot-11 1/2-inch tall woman? And construct a table and chair for her proportions? While having rooms the right size for her is believable (Insectosaurus's presence proving they deal with giant monsters occasionally), having the rest of the stuff on hand is stretching things beyond Crazy-Prepared.