Sc heads will work.
All of the passages and what not will work. Changing the Cooling and oiling passages would have required a rework of the block.
The heads are stouter and can handle the rigors of the supercharged world better than the N/A heads can. I don't know the size comparisons of combustion chamber size SC/n/a. Nor do I know valve diameters either comparing both heads.
Intake and exhaust manifolds should bolt up fine. I think that the only real change that was made to the SC heads Vs. N/A was that ford added material in the castings for the cooling passages to stiffen the heads up. Of course this slightly impacts the cooling capacity of the heads.
What I would suggest is you either take two routes. If you can get a set of SC heads cheap, make sure to have them P+Ped real good. But have them done for a N/A enviroment (good intake tumble and swirl, velocity)
Now another option would be to use the Split port heads from a 99+ 3.8 Mustang. In order to use those you will need the split port intake. I think injectors from the Mustang will work, but you might have to do custom work on the fuel rails to make it fit.
The split port design is great for both low end torque and high end HP. Exhaust ports are smallish, and even with extensive porting only yeilds minimal results but then again, you are not inducting as much on the intake side either.
One member here named "gaston" has done this swap and then plopped a Vortech on it. Making in excess of 400hp in his mustang. He might be able to offer more insight. Don't give up though, I seriously think that a great high winding 3.8 (or 4.3) stroker is possible in these engines. Especially if the owner does great work to carefully balance everything and reduce rotational mass.... Good luck and report back often if you do decide to use S/C heads.