Hi Wayne,
Yes, we did have to do some minor die-grinding on the intake pushrod holes for clearance. We also had to mill the manifold to fit. IIRC, we had to take .025" off for the ports and bolt holes to line up. The intakes flowed 337 CFM @ 28in. I don't remember exactly what the exhaust flowed but I think it was in the high 250s. I'll have my buddy look through his paperwork. The heads used standard face valves, (no tulips) I also mis-quoted about the intake work. It was port matched and had some minor reworking of the port floors. (I have too many motors floating around in my head:
I don't think milling the top of your intake 1/2" will hurt very much although a motor of the size you (and I) built definitley likes big plenum areas. I guess if you want it all to fit under the hood there isn't much choice!
--Mike