Not "one", two.
So here's the deal. I currently have Indy EZ1 max wedge heads and single 4 intake. My pistons sit .016 out of the hole and I have the thickest gasket I can find and still only have .035 quench. Close enough to be nervous. Now I've got a hankerin' to install efi using the Eddy Pro-flow intake BUT its made for standard ports so-o-o-o I'm thinking if I switch heads to a standard port at the same time I'd use an open chamber and solve my quench issue. But obviously with .100 its going to be far to much clearance even with a thin gasket. Yes, I suppose I could cut a brand new set of heads !!
The most cost effective solution to your problem which depending on how much piston to wall clearance you have, might not be a problem, is a Cometic head gasket and a trip to the machine shop with your intake to have injector bungs installed. Lots of change from that out of the price of cylinder heads and a new intake.
Depending on where your top ring is located, shaving .004 off the piston shouldn't compromise its integrity but head gaskets are still cheaper and easier.
That Proflo intake with the front mount throttle body does look cool... Your current combo has more power potential tho.
Kevin