Ive heard horror stories about mr gasket head gaskets leaking. So if i had .040 taken off the heads, i would have to have the intake milled? Thats only .005 or so from stock. Machinest quoted me $80 per head
I've used the Mr. Gaskets almost exclusively for years, no issues.
Gasket failures are usually the result of improper installation or bad surface prep.
The machinist should be able to tell you how much needs to be taken off the intake or the head at the manifold surface. I'd look it up for you, but I'm tired and I'm going to bed. Take the cut off the heads at the manifold surface. If you take it off the manifold itself, you're married to that manifold. If you ever want to change manifolds in the future, you'll have to have them cut, too. If you cut the head, any stock manifold will still fit.