1. You don't need to wait to stain it. It's better to do it now. No need to "dry out" the wood or anything. In fact, if you wait a year, it will turn gray, and you'll have to do a bunch of prep work to get it nice and pretty to stain again.
2. I'd use a stain that, to refresh down the road (and every deck will need that at least every couple years), you can just apply like stain over top of it. You don't want to have to strip and sand it down each time. TWP makes a good stain that you can do a build-up coat on, like 3 coats now, then a top coat every year, with just a good washdown and dryout as prep.
3. Replacing deck boards is pretty simple. The key is just to keep straight lines. Get a bow wrench to help you persuade non-straight boards. And stop every few boards to measure the remaining distance from both ends, to make sure you're progressing evenly. If not, adjust the normal 1/8" gap as needed for the next couple boards to make the difference back up.
If it's 25 years old, it was built to older codes, so while the frame is exposed, I'd take the time to upgrade the structure to comply with current codes and be safer. Things like joist hangers and hurricane ties, make sure the ledger board is secure to the house, consider beefing up the posts from 4x4 to 6x6, make sure balluster spacing is <4", that sort of thing. It's hard to tell without photos what you might need/benefit from, but the American Wood Council publishes a great guide to deck construction, and you can compare what you've got to that:
http://www.awc.org/publications/dca/dca6/dca6-09.pdf
