Since no one could answer my question.. I answered it myself I got my 99 Cobra this weekend.. First thing I did was tear it apart to replace the broken T45. I had gone and bought a used T45 the weekend before. I really couldn't pass it up either way for 50 bucks. So, anyways.. after about 45 min getting everything loose/out, I spent about another 12 hrs working on the top-right bolt from the bell housing to the block... I ended up grinding the head off and just replacing it. Anyone else had this problem? One of my friends told me he had the same problem with his 00 GT. After getting it out.. I compared the T45's and ended up swapping the speedo gear for the metal gear out of the old T45. Swapped tail housings, and bell housings. The other bellhousing would have worked, but it didn't have some of the structural support that the Cobra housing did.. I am guessing the T45 I have came out of a GT(96-98).
Everything is back together good and I just have to put the exhaust back on probably tomorrow, then be driving it.
I know this T45 isn't going to be as strong as the other, but I just needed a quick fix so I could start saving for the T56.
I hope this helps someone else that may end up needing the same quick fix I did..
Yeah the 96-98 have differnt mounting points. I ran into the same problem when changing out my 97 T-45 to a 99 they had to buy another crossmemeber I think. I was out to sea so I am not 100 percent sure