I'm thinking you should countersink the screw holes in the Indy valley plate so you can use flat head screws to hold it down and make the seal needed. If needed, mill a little off the top of the plate if it hits the intake anywhere or have a custom plate made up. I think AndyF makes a billet plate that might be thinner than the cast Indy plate. I wouldn't hack the intake. Sounds like more work than the plate and then you have an intake that only works with those heads. The plates are cheaper than the intake.

http://arengineering.com/home-page/valley-plates/

It doesn't look like Andy has a Hemi plate, but I'm sure he can fab one up for you. You won't need the access holes for the Hemi, so maybe you can save some money and have him make a one-piece plate.