I had to scoot my Magnaflow y pipe back as well to get the bends to fit. Ive seen some people cut the stock exhaust behind the 02 sensors and then ran it over the cross member and the across to the passenger side to the y pipe. The stock exhaust section under the transmission is flat at the top to allow some clearance and also to help from creating too much heat. Here are some pics of a setup that I like.
http://ramforumz.com/showthread.php?t=71908