I'd hammer in all those nails and prehaps add some screws. Loose nails in a subfloor will cause squeeks and when the flooring's off is the time ward them off.

You can use an old t-shirt over your broom to wash it. Put the shirt over the broom so the tail is down and the neck is on top. If the neck is too big for the broom then pin it with a safety pin. When you wet it wet it just until the broom bristles so they don't get too wet. You only want the tail of the t-shirt wet. Put the tail out on the floor as far as you can reach, and pull it towards you.

If the subfloor has urine soaked into it, find one of the cleaners meant for de-stinking urine stains and apply it.

Then let the stuff air-dry before you do the new carpet.

Target sells some stuff called "Kids And Pets" (or "Kids & Pets" not sure) that has worked great for me for potty training accidents on carpets and carseats. It actually does get rid of the smell and it's very convenient in that it doesn't require rinsing.