What level components are on your MTB?
1. - Can't help there.
2. At the very least, they should have you on a trainer for 20-30 minutes, and they should make some adjustments to the bike to help with fit.
3. Dunno.
4. They'll be happy to swap the crank for you. Expect to pay full retail for the new crankset, and maybe get a deal on labor. They legally can't sell the Bontrager set as new once it's off the bike, as from what I was told, they need some sort of license to deal in 2nd hand goods. My advice? Learn to like those cranks.
5. Pedals are easy to screw in and up. One side is reverse threaded. Even someone who's been tinkering with bikes for 30 years (not me, of course ) has been know to strip pedal threads. A saddle is an easy swap - getting it properly adjusted takes more time.