Dan,
the stock pieces intakes and heads are restrictive. If you change one or the other you are just really moving the bottle neck of the system some where else. Now since I know you have that sweet set(
nobody else ever gives you the credit you deserve) of ported E7's I would port the lower intake and or atleast port match them to the intake so your flow has a smooth transition. The Holley Systemax I lower does as stated by Moxie straightens the runners out. As far as the Cobra intake not matching the E7's very well, I have never heard that before, now I know they were made to match the GT40 style heads but if you port match them it won't matter anyway. Dan if you attemp porting the lower just be careful not to break through on the runners I am not sure exactly how much metal is there, but if you do I have 2 of them laying around. Keep polishing away buddy...
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My Ride Check Out My Site 91GT, Holley SysteMAX II Kit-Heads 2.02" x 1.60",Full MAC exhaust 1-5/8" Long tubes, 2-1/2" O.R H-Pipe, 2 1/2" cat back, 12" K&N Filter, RNH PERFORMANCE Ram Air, Ron Davis Radiator, Full Suspension,3:73's, Welds, Best on new motor-12.60 @ 108, no traction 1.98