Cylinder head flow vs Intake valve size, Beyond my knowledge Options

[lmcchesney]

I want to start off by stating I am not a experienced/knowledgable engine designer (IMG:style_emoticons/default/confused24.gif) and also want to thank Jake for the email alterting me to the discrepency (IMG:style_emoticons/default/burnout.gif) .
I have a 94mm x 78mm stroker crank with a Web 73 cam. P and P heads but it was suggested by the engine builder that I go with 48mm intake and 38mm exhaust. The builders are fairly known race engine builders for VW and others, but predominately in the short track circuit (outlaws, circuit, etc.)
I have been told that the 48mm intakes limit the rpm of the engine despite the builder stating that the engine is an 8,000 rpm engine build.
My questions are:
A larger intake valve would increase the volume of air flow or less resistance, so how does that decrease the potential rpms.
If as it seems to be a fact and I want/need a higher rpm engine, can it be adjusted for with a programable ECU like a megasquirt?
Or (IMG:style_emoticons/default/dead horse.gif) do I just need to rebuild the heads with smaller intake valves and what size is optimal?
Thanks,
Larry