with the exception of one block being aluminum and the other being iron, they are made the same and use the same bell housing so the tranny thing is an easy swap. How complete is this motor you have? You said 98 4v, is it from a cobra or a Mark? I'll just tell you my 4v swap is from an 01 cobra and they're a little different, but i'll try and help you however I can.
You will want to reuse your gt engine harness, it'll work just fine. Also keep the gt computer. It will of course need to be dyno tuned professionally. You will need the fuel rails from the cobra, as well as the throttle and cruise cables. They are longer and your stock cables wont reach. You will also need all the radiator hoses from the cobra along with the thermostat housing. They are different from the gt. Im going to say you will need the MAF meter from the cobra. Im not sure on this, because I don't know if 96-98's came with 19 or 24lb injectors. Im gonna say they have 24lb, if so you will need it.
As far as wiring, I didn't have to extend any wires to make mine work or anything like that. Some people have done it without extending wires, some say you must. I didn't, but who knows what you'll run into. The only thing I had to do was ground my alternator, but being that yours is a 98 I don't know if you'll have to worry about that or not. The only other thing I can think of that might be a problem would be the second coolant temp sensor. 96-98 gt's have 2 coolant sensors, one runs the fan while the other works the temp gauge in the cluster. I don't know if these model cobra's have a second coolant sensor or not. If not it will be necessary to add a second sensor to get your stock gauge to work. I did not do this, as I don't really trust my stock gauges. I installed an autometer temp gauge.
Thats about all I can think of right now, I gotta go do some things. Post up and more questions with specifics that you have and i'll help all I can.
