He made that so called "drop" modification to net you a difference of about .007? That's what the math calculates out to. That's absurd. Now you have a gap, an area, or a void that is between the protruded portion of the cylinder head and the cylinder. To avoid detonation you tighten up the quench area as much as possible. That means if you effectively, and correctly measured .032 and .037, then the only area that should have material removed is the cylinders base, and no where else. That amount that needs to be removed should have been anywhere from .035 to .037 on one cylinder and .030 to .032 on the other cylinder. This method prevents detonation because it forces the air/fuel mixture to the pistons center, for the combustion process.
As far as the torque instructions on that paper posted, it's horse shit. The 90 degree method is bullshit and the least accurate. Polish the o.d. of the head bolts shoulder. Use moly on the shoulder, use moly on the threads. Torque the 4 bolts to 17 to 18 ft pounds, then to 32, and last torque at 40. Between torque intervals, let sit for around 2 minutes or so, as this settles the gasket. Pull the torque wrench slow and steady, and if you want to throw an additional step in prior to the 17 to 18 initial torque, you can do so with 10 to 12 foot pounds.
My opinion on your cylinder head machine work is, to surface the heads flat, period. Get rid of that step.
Check your manifold to port alignment and correct if necessary.
How the heck are you suppose to get rid of that tic if you didn't make adjustments to the rocker boxes?
Did you put new lifters in this engine? If not, my suggestion is to put a brand new set of S&S premium lifters in it. The only way to figure this out, is to discard the old and put on new. It's only two cylinders and not a V8. Things just don't correct themselves by wishful thinking.
P.S. I have head gaskets that are .023, .030, .035 and .040. When you think about what was done for .007 of a difference, it's crazy logic and makes no sense what so ever.