The hood clearance issue is if you use a cobra intake, bit taller than the stock intake. I'm not sure why the changed the intake over in 97, the earlier design seemed to make more power... speculation from blowing them away with my 95, could be a less aggressive tune, I'm not sure.
It would be a worthwhile swap if you can find a moderately low mile DOHC for a decent price. It just seems like you'll either be tearing into a $3000 Mark VIII to find one with under 100K on it or getting one with 150k + on it.
Adding some long tubes onto there will tack on another $500 to the price and you'll have to do some surgery to them, more than likely, most definitely will need to modify the position of the steering shaft.
If you're planning on a super charger, a low mileage 2V PI motor will give you the best bang for the $. There are a few kits out there... I think.. it's been a while.