You should check out the fordsix forums. They got some wizards up in there.
From what I've read, the EFI head doesn't flow as well at low valve lift, combustion chamber is smaller (higher compression), combustion chamber shape is "fast-burn" for fuel economy. They are also prone to cracking. There are new manufactured ones that are more stout and big valve CNC ported ones as well. No such off-the-shelf improvements for carb'd heads that I know of.
You might need to look into what cam to run.
I'm also doing the research for a build/rebuild on my own 300: carb'd head with big valves, porting, cam, aftermarket intake manifold, EFI exhaust manifolds, and Holley Sniper EFI.