Any tuning guru's out there?

I have a stage one ported head on my car that was fitted with a Thurock 2.0 8v engine by Volkspares.
I recently fitted a polished inlet manifold and noticed that the inlet ports have been ported out larger the the gasket and therefore the inlet manifold ports.
This has created a trough at the bottom of the ports in the head which i think may cause turbulance and therefore reduced gas speed.
Does anyone know the effects of overporting the size of ports on Cylinder heads?
