Porting is not something I would consider unless I intended to go FI.
If so then check here http://www.miataturbo.net (only read, do not post, far to rabid)
There is more horse power to be made with the 99 head.
There is more torque from the VVT 01-05 non MS head. Bell Williams is racing and uses a VVT head with a square top intake manifold, or at least did, successfully.
For parts and opinions check out 949 racing http://949racing.com/engine.aspx
My 2c