HEADER CLEARANCE PROBLEMS....HELP

Im in the process of building my car 1990 GT hatck, and installing used BBK 1-5/8" long tubes. I installed motor with the longtubes at the same time, then went to put the transmission in yesterday and found the collectors were too close to get the bellhousing in. So I loosened both of them up wiggled it in then tightened the headers back down. Heres the ****ed up part....I cant bolt the bellhousing to the block because the shift fork is touching the header, alot. It appears as if the header is bent, however the ceramic coating still looks great and none of the tubes are bent or dented to show signs of any impact what so ever. The engine and transmission are out of a 1995 GT, but I dont see any reason why the trans would be any different, unless the bellhousing opening for the fork is in a different location. I need some help ASAP.......

Thanks guys got it figured out, so heres the story......94-95 T-5 transmission is different by the input shaft being 1" longer to compensate for the loner wheelbase. Because the trans is longer they made the bell housing different by lowering the point at which the shift fork leaves the bellhousing. So now i need a foxbody bell housing, input shaft and shift fork........anyone got one for sale? Also I will need the shorter the bearing retainer by 1" ughhhhh **** I just want to get this car done.