Pretty sure the general consensus here would be that it's not really worth it to upgrade this bike to the extent that you are planning up upgrading it. You've listed at least a couple hundred bucks in new parts, for which price (with a little careful shopping) you could have a better used bike from ebay or craigslist for a lot less manual labor.
If you are determined to do it...
1) yes your wheelset should take 8 or 9 sp cassettes
2) # of speeds if you don't have an FD is really just a matter of taste, and the terrain you ride on. Doesn't matter too much, but unless you bike in a pretty flat area, I suggest a reasonably wide range, maybe 17 - 19 teeth total difference
3) not sure about 9 sp cranksets versus other