Best transmission for 98 cobra?

I have a 2003 gt swapped with a 98 cobra. Currently the transmission is cracked and I’m just wondering what trans would be best to replace it and if I could get a stronger trans, what would properly bolt up to the 98 cobra and the 03 gt?
 
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Most likely its a stick. A rebuilt 3650 is what I have done and would do again and will do again if/when the t45 in my 2000 goes. Get ahold of Stan at Pro Force Performance in Atlanta. That will ensure all the fixes are done and you can choose the .68 or .62 overdrive.

Had a fully fixed stock rebuilt 3650 in my 98GT and that was legit the smoothest best shifting trans I have ever had save maybe the low mileage original T-5 in my old 95 Cobra. 3650 gears are beefy and with the fixes done the weak point becomes the 10 spline input which is good for about 500ft lbs. Get a 26 spline shaft and they are good for even more.