On my swap, I used the same motor mount spots (Front holes on block, a t56 magnum and the 04 cobra driveshaft and it all bolted up perfectly. Just as it had with my 2V motor (I had the t56 magnum and cobra shaft pre-swap).
So, if you can use a t56 and cobra shaft in your car right now, I don't see changing the engine affecting that.
i didnt have the engine in the car so i couldnt measure it. now it is all in and the stock T56 driveshaft works perfectly. i have a full trans setup from an 04 cobra in the car