Shane is right, I have done the swap and here is the post that I put up on many Mustang boards back in September 2003, for everyone interested in doing the swap to their Cobra.
Info for ’03 T56 Swap Into ‘96-’98 Cobra
Here is all the information needed that I have gathered from various spots and put together to do ’03 T56 swap for ‘96-’98 Mustang Cobra's. I figured that this would help out anybody that is considering doing it and need to know what is involved to make it work.
1. The stock clutch can be used. because the spline count on the input shaft is the same
2. The stock shift fork and throw-out bearing can used, if there is none that come with the new trans.
3. The pivot ball stud that comes with it is the one to use.
4. The stock crossmember needs to be moved up an inch, by using the front bolt holes on the mounts as the back ones and drilling new holes were the front ones are now at.
5. The stock driveshaft will have to be shortened 1¼”, rebalanced and have a new yoke put on it that is a 27-count spline to match the tailshaft on the new trans.
6. Use a SpeedCal that is calibrated with the new ER, extended range, version for the speedo Connection, otherwise the speedo is going to read way fast.
7. For the back-up lights use the one from the T45 and simply just crimp the inside connector smaller and it will work just fine.
8. For the reverse lock out solenoid you have three options that you can go with for this. You can use a harness that D&D sells to connect to it or you can just leave it alone and not use it, but it will take two hands to get into reverse, or there is a article on stangnet.com in there tech articles on how to power it from the brake light switch and use that to make it work.
9. For trans fluid there is a variety of different types that you can use and I will list some of the ones that I know work good in it. Royal Purple Syncromax or Redline ATF D4, or Ford Mercon Dexron III. Also, fill it up with fluid until it starts to come out the fill hole and close it up.
10. The long black tube with the white end on it is the vent for the trans and should not be removed.
11. The stock trans mount with everything bolted to it from the T45 can be used for the T56. To make sure that the new trans is straight just eliminate the plate that has the exhaust posts on it for holding up the middle of the h or x pipe on it.
12. You can use the stock shifter that comes with it or you can get a Pro 5.0, Hurst, or Steeda one instead.
13. All wires that connect to the new trans will be long enough to reach the new locations and is a good idea to route them over the trans and not under it. Also, the exhaust that you are using should have no problems with clearence or space problems.
The swap is fairly easy to do, but will be much easier with two people doing the work. The good part is that it requires very little new parts that are not reused from the old T45 trans. If there are any questions please feel free to email me and I will try to help you out.