I bought a 96GT will a blown motor and was planning on putting in a 96-98 cobra engine. I'm not going to have the money to complete a cobra engine swap and decieded to go with a PI engine swap.
You can use your GT PCM but will have to have a tune because the cobra engine has IMRC which opens butterfly vavle in the intake manifold at 3250 or so for better gas mileage and more low in torque.I done some reading on this swap but never found all the info I needed. Motor will fit fine, use cobra wiring harness and GT computer so your PATS will still work and the info above will be needed from tune or you will not have the full potential of the swap.