Porting is definately the only way to go on a blown motor, smooth the intake runners an match port the intake to the heads. Exhaust is definately where the most power can be gained. Valve pocket porting very important and make sure the headers/zoomies are big enough, i would say 2 1/2" min on a b/blk.
With a roots supercharger you will definitely be limited by the maximum boost pressure and maximum Rpm the supercharger can be turned. There will be far more to be gained by reducing the total back pressure after the supercharger, and that includes the cylinder head, induction system, intercooler, camshaft and especially the entire exhaust system.
Anything that causes chronic supercharger constipation is really bad news for airflow, and trying to improve the blower itself is going about it the wrong way.
Build yourself a traditional high performance engine, but with suitable cam and compression ratio. You will make more Hp on less boost, and much lower thermal sress on everything. Let the whole thing breathe.
The greatest initial gains are usually made with the exhaust system. There is roughly a 1:1 relationship between boost pressure and total exhaust back pressure. Reduce exhaust back pressure by 4psi, and boost falls by roughly 4psi.
You then turn the supercharger faster to restore the original boost pressure. Flow increases, power increases, but induction temperatures and the detonation threshold stay about the same.
just my .02
Zip.
I don't know anything about trick flow heads except i have a set of street versions on my Elky.