I have done this swap, you will need a 03 cobra splined 10.5” clutch, you will need a different output spline for driveshaft, the mounting is not a big deal, but driveshaft length changes too. I run a HD Ford Racing 03 cobra shaft. My trans is unique, as it came to me second hand from a guy who had it built to bolt into his 99 Cobra. So mine uses factory splined input and output, so I have hybrid U-joints connecting my factory yokes on either side of that 03 cobra driveshaft. Mounting was not a big deal, I believe I just changed to a stock style urethane mount when swapping. The reverse lock out can be an issue too, either remove it, muscle past it, or wire it to a switch / brake pedal ( risky if you downshift under braking).
Now the speedo can be a big deal as in 99 they changed the pickup and signal type. 99+ is a mag pick up, factory is a gear driven Hall effect. I used a DM speedcal for years to great effect to translate and calibrate then new sensor signal to the factory dash. In storage, the DM box fried and the company is now belly up, so I’m currently searching for a solution there.
So, short version - factory 03 Cobra t-56 - input and output splines are different, driveshaft length is different, speedo pick up is entirely different. Bell-housing is unique to the T-56, but the factory one for the 03 cobra works just dandy on our blocks.
There are custom built options if you are ordering a new trans. You can get it with 97 factory splines input and output, as well as with a 99’s style gear driven sensor installed. With that option ( it would come with a bell housing as well) all you would need is to shorten the factory driveshaft and decide what to do with the reverse lockout.
Hope this helps, it’s all based on memory from about 12-13 years ago, but I’m generally pretty good with remembering details like this.
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