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Im not a mustang guru so forgive what Im about to say as a well intentioned trans guy who is blue oval stupid.
Check your input and output splines and make sure they're what you can work with. Check your LOA (length overall) and the length and diameter of the input shaft. Id also check the LENGTH of the splines to make sure you have enough to get the job done, and of course pilot dia. You can also give me the sheetmetal tag number on both units (should be 1352-xxx-016 for example or a for letter and 4 digit code like TUET4167) and we can compare gear ratios. Id also recommend looking up "Bad Shoe Productions" on the googles. That fella did a great job of a T5 rebuild. You may find that rebuilding the factory unit in that car is your best option. I can help you source parts if need be, or turn you on to a rebuilder, however they're not hard to do with some reference material, a clean surface and a plan.
Note, check your crossmember mount.
I doubt most of the things referenced above will be changed, HOWEVER, this is good info for any trans swap. I'll grab a catalog at luinchtime and see what I can find info-wise
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