Finally, my first 360 and goals for it! I'll be asking a lot of questions.

Your machinist must not do performance very often. Years ago I had a machinist say the same thing, he went blah blah blah and I said do it anyway. He did it and put on the receipt really big "cut .040 at customer request" and I had to sign it. LOL..... That project was about 20 years ago and those 360 heads are still on that 318 (I know the guy I sold that Dart to) and runs fine.
Now that the heads are removed I measured the gasket that was installed, it was about 0.035". I put the heads back on without gaskets and then put the intake back (with the gaskets that mounts to the heads, not the china wall). The intake now hits the two pins on the china walls. Do I remove them, if so, how, do they pull out with a plier?