4.6l Dohc !!!

It can be done. A good friend of mine put a 4 valve 5.4 in a gt and used all stock type cobra parts like wiring and puter. He had to make a custome upper intake as none were avail at that time. Its really cool looking and different, but as it sits un tuned, it runs 13.70s at like 102, so basically runs with good bolt on pi 2v's. Tuned, I imagine it runs a lot better but it was a lot of work and he is very mechanically inclined.

Why dont you put your top end parts on the alum. block. That block should have flat top pistons and should bump your comp. ratio. While your at it do a port your heads and get a nice set of cams while the heads are off. Put it together get a good tune and you will still be below your 4v swap budget.

Okay, dont hold me to this but I have read many swap posts in this and other forums and this is what I found: The engine will drop right in and the stock computer will run it but needs to be flashed. The IMRC wont work so you eaither need to get the bypass kit (or remove the blades) or find the adapter kit. Somebody on here knew where it was, I will see if I can find who.
You can also use the Mark VIII plenum but need a cowl hood to clear it. Your best bet would be to get a 96-98 Cobra plenum and drop it on. They can be found for $300 on eBay. Because the Mark VIII is a six bolt crank you can use the GTs flywheel and clutch just fine. With the Cobra plenum you will have 90 horses over your 98 GT motor has but the DOHC has a much nicer power curve, revs higher, builds torque quicker and just sounds so freakin sweet!

I have outrun SN95 Aeros and New edges as well as S197 GTs at the track so the motor has some balls

Yes, for the most part that will bolt right in. Might as well get a 96-98 Cobra intake as they bolt on the B heads of the 93-97 Mark VIII. You can also do a short runner intake w/ a IMRC delete(you will need to 4.30's or more to overcome to the torque loss) and enjoy more mid-high range power w/ tune.

You might need to modify the wiring harness, but not 100% sure. Also I would find some cleaner coolant crossover tubes as yours looks in bad shape. Being the engine is out, I would try and clean up(replace if you can while it is easy to get to) some parts. Much easier now, than when they break and already on the car.

i just picked up a mark viii motor and trans for 250 total!!! im going to work on converting my hatch to a mod motor. i primarily got the motor for the heads, block, and accy brackets....
it is very very very pricy swapping to a mod motor w/o a doner car

the trans is going to be rebuilt and put into my convertable w/ a trans brake

did you take progress pics and stuff? i as well as the rest of this community would love to see them and even possibly a write up

-excellent work