Interesting thought!
Whats your port configuration barry? The engine I ran on the two setups outlined above is a stock port...for the most part. I cleaned up some casting and added a little shape to the bowl, and brought the intakes UP ~2mm on primary and secondary.
Exhaust was slightly widened, and brought DOWN ~2mm.
Stock overlap (S5 TII block)
Also, on your point of running different size turbine housings, note that I did step up from .84 on the old turbo to 1.00 on the T04-R
EDIT: That stock port engine is currrently being "refreshed" and I'm thinking of going a little larger all around on the exhaust to promote better evacuation of those hot gases, thoughts on that?