Yes, one muffler is longer then the other. Ford engineered them that way to rid any "drone" from the exhaust. I put a MAC cat back on my friends 90, and it did the same thing. Ended up having to have an exhaust shop put a 2 inch extension in the flowtube.
Why do fox owners have so many problems with MAC catbacks?
Mine went on fine. The only problem is that the tailpipe's a little close to the gas tank on the passenger side. Still gotta take it off and adjust it with a hammer...I'm just lazy.