Good job! 6 miles in 35 minutes is a pretty good time.

First few weeks is where most of the hurt will be. After that you will start to acclimate and it will get easier.

Anybody point you are Sheldon Brown's (RIP) site? http://sheldonbrown.com/beginners/index.html He has a good section about "pain" and how to adjust the bike to take care of most of it.

Get your rack sorted out?