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I would assume that the over axle pipes are the same. Dumb question, did you loosen the bolts on the flange to the intermediate pipe. When I put mine on, those needed to be loose until the tips were aligned then could be tightened. If you did not loosen those, that would be my guess.
I just did the same thing and found that I had to replace the over-the-axle pipes. The lengths are a little different and it seems the hang a little lower than the previous "overs".
Also, I dumped the clamps that come with the PRTs and used the standard 2 1/2 inch U-bolt muffler clamps. I found the BB ones never tightened enough to keep the mufflers from moving. The U-bolt ones worked great!
When I put BB Rte 66 Quads on an 00, I had to put shims under the hanger to allow it to hang down far enough to the fowl muffler so the quads were straight horizontally. I used 3/16th thick flat washers between the chassis and the top side of hanger. Did use the furnished clamps and air gunned them on, couldn't find 2.5" stainless U's.