I don't have the time to im you while you are doing it, but I can try to help here. What are some of your questions?
Google around to find out where your iTunes is storing your iPhone backup. Save it somewhere else, it might come in handy later. Before jailbreaking, most of the time I just gave up and resorted to the fact that I was going to loose my high scores, and a few other bookmarks in apps and such, but most of my other apps sync with the cloud so I don't loose too much data when I set my phone up new. But in theory you can get your itunes backup of your phone extract certain data and after you jailbreak ssh into your phone and copy some of it back.
Follow the instruction for jailbreaking and do it. Worse case scenario, you have to do it over again. The pwnage tool for 3.1 is pretty straight forward. iClarified.com has some nice tutorials.