1. I don't know. We're kind of in the same boat here. Just upgraded. I went from 26" tubes to 29" tubeless and it's fantastic. Can't say for sure if it's the tubeless or the size.

2. I bought both my bikes from Craigslist, both a couple years old but barely used. Bought a $520 bike for $300 (over 40% off from a new) and learned to ride on it (rode for years). Great for what I paid and needed. Just bought a $2,000+ bike for $800. True, a LBS should be able to fit you up better for the ideal bike, but for the kind of deals on Craigslist I'll be going with a 'close enough for me' fit from here on out. Plus, if you have an idea of what feels right, you should be able to do the same.

3. Fork and frame. I don't know anything about wheels (but they are pricey).