Right, Paul, Athena head gaskets are 1.5 mm. (.060") thick, ~.017" thicker than OE. OP, deck height is deck height, doesn't matter if you get more at the top of the barrels or at the base. If you want to use an OEM Yamaha or OE spec Vesrah head gasket, just double up two base gaskets.
But that isn't usually necessary on an XS650 motor with the deck lowered only .020". First off: don't worry about valve-to-piston clearance. You'll have plenty. The potential problem is squish clearance--clearance between piston edges and the squish band (the chamfered edge of the combustion chamber). Here's how to check it. First bring the pistons about halfway up the cylinders. Using a dab of heavy grease to hold them in place, lay a short piece of .050" rosin core solder on the exhaust side and the intake side of each piston, pointing toward and just touching the cylinder wall. Remove the valves and assemble the head, camshaft, and rocker cover on the motor. (Don't bother with cam timing; valves are out, the cam is just there to keep the cam chain from locking up). Slowly turn the motor through TDC. Measure the thickness of the solder strips where the pistons have pressed them against the squish band. If they're .040" thick or more, you've got no worries. Remember: lowering the deck will retard cam timing a bit, and any cam-driven ignition with it. You may have to get creative if you run out of advance side ignition adjustment.
BTW the head didn't warp because the gasket blew; the gasket blew because the head was warped. I've seen XS650 rocker covers warped due to cave man maintenance, but never an XS650 head. There's a first time for everything, I guess.
