Any 5.0 tranny will bolt up, you just have to use your existing belhousing.
A rebuilt tranny will cost apporox $1500 after install. To have a shop rebuild your tranny will be just a hair bit cheaper. A quick syncronizer redo will cost a heafty pinny as well.
Mustangs Unlimited - The Premier Source for Mustang, Shelby and Cougar Parts and Accessories sells a rebuild kit, that way all you have to do is bring it to a shop and have them do the labor, that way you miss out on the charge for parts.
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Trinity 99 Mustang SVT Cobra 280 rwhp, 290 rwtq
Selena 95 Mustang SVO GT-40 250 rwhp, 275 rwtq (Under Reconstruction)
00 Mustang V6 (sold)
98 Mustang V6 (sold)