I don't know if you ever found your answer on the best way to upgrade, but I had the same issue myself and was hesitant to try because I was confused about the status of the GPS after going custom. However, I followed these instructions to the letter:
http://forum.xda-developers.com/showthread.php?t=472805
and all worked out fine.
It's CRUCIAL you downgrade first using the first link in the first post, and then roll on. The 2nd post has points you to the wiki for getting GPS going using qpst.
It's a must read.