Exhaust vs Trans crossmember

Sounds like they installed the wrong T45

If I remember correctly, there are two different types of T45s for the Fords. When I was looking for a new one, I called Smart Auto Parts, and the guy said I needed to measure something (can't remember what though) to make sure I get the correct one. Call them and ask for help @ 1-888-995-PART. Below are links to their Mustang reman trannies if you want/need another tranny (I found they had the best price and a six month warranty). Keep in mind, the T45 was replaced in 2000 with the Tremec 3650 (the T45s are not strong enough for aggressive driving). At a MINIMUM, get an aftermarket shifter with positive stops to save the shift forks. I believe a world class T5, TKO or T56 would be better choices if you can swing the dough (you will also need a new bell housing as the T45 has an integrated bell housing)

http://www.smartpartsauto.com/manual_transmissions_mustang_t45_2870.htm

http://www.smartpartsauto.com/manual_transmissions_mustang_tr3650_4014.htm

http://www.smartpartsauto.com/manual_transmissions_mustang_t56_4106.htm

As far a solving the problem with a new x or h pipe with cats, I think they will all end up in the same general location as the stock ones. Perhaps switching to longtube headers and a matching x/h pipe would offer more clearance (and more power!).