I wouldn't think so... maybe some tweaking would be necessary for speedometer correction? What part of a manual tranny is controlled or monitored by the EEC?
However you possibly will need a different trans support, drive shaft, and clutch. The 03/04 Cobra T56 uses a 10-spline input shaft.
i really wasnt sure if any part of the manual tranny was controlled or monitored by the eec but before i got in over my head and had to spend a lot more than what i was expecting i wanted to make sure. Thanks for your help
I swapped a T56 from a 98. I used my same clutch since the tranny input shaft was 10 spline and so is the 99 and 03. So you could use your same clutch unless you want a stronger one.
Not sure about the speedo though, I needed to buy a speed cal from DallasMustang. They are cool so call them and tell them what your doing and they will help you decide if one is needed. I think it was like $100.00
Also see this site it shows the 3 types of speed-cals
Forgot to add. You will need the drive shaft with that T56 and you will need tranny support as Uncle Meat says. I just had simple braces built for me. I dont think you can use the 03 tranny support on your 99.