[akstrohm]

First of all, guinea pigs are active day and night. So covering the cage is not likely to have an effect on their behavior. It will just reduce air flow.

Secondly, I would wait until the pigs are past puberty before reintroducing them. The last thing you want to do is introduce them and then separate them over and over again--that will just make them less likely to get along in the end. The new cage you have planned sounds excellent!

Guinea pigs don't rely too much on sight. They have a much better sense of smell, so as long as they are near each other (which is best for them), the dominance behavior will probably continue.

I wouldn't bother getting new coroplast unless you want to. Vinegar will work well enough for cleaning it.

Are you sure there is no way to move the cage to another room? That seems like the only way you are likely to get more sleep.