hmm, well... unless i'm getting radical with crazy stuff, i line up the piston to the bottom of the transfers, there are some theories about minor misalignment in the transfer-to-piston-crown interface leading to badness... there are also some theories about anti-reversion stuff that says its good to have a misalignment there... woah! too much thinking for me, i just set my cylinder base spacing to get that perfecto, then i port the exhaust to match. Usually i let the piston crown dip a cunthair below the exhaust port floor, just so i don't get a hot spot on the piston. maybe i made that up, maybe it works, i dunno, my pistons run pretty cool.
if you've got fancy schmansy head machining stuff, you can cut your head to compensate for whatever the deck height comes out to, or machine your cylinder. If i don't have that equipment, i get it close or would pay someone to machine my jug if it was super far off. You can fix your squish a little bit with the head gasket, but you gotta use good ones, aluminum or copper or whatever. Beer can is ok, but copper is better.
i haven't really seen too many of the commercially produced heads that i like, i think they are set up for high rpm AV10's with crazy exhaust timing. I prefer something with a smaller squish and a bigger taper. 1.0-1.3 squish clearance is usually what i'm shooting for.
As for the temp thing, i'm assuming you mean CHT... this is tricky, not an easy answer. First of all stupid swingy french motors run hot head temp because they don't get good airflow. Second the fins are small and third they are variated so they are ripping high RPM when not moving very fast and getting good cool air.
The piston temp is really what you care about, not the cylinder head temp. You can get your CHT up to 700 degrees where aluminum begins to loose strength, without causing any harm to your engine.
if your piston face gets hot, however, you will sieze... bummer.
If you're careful to keep your piston cool, 400, 450, all day long on the CHT. If your piston is hotter than your head for some reason you can sieze at 380.
I watch the piston face and underside for black carbon buildup. That means your oil is burning and you're piston is 400-450 degrees. If you're paying attention and notice your temps are consistent, say, 410, and your piston isn't building up black carbon, you are safe at that temp and can assume short blasts up to 420, 430 are safe. If you are running 390 and getting a lot of gunk on the piston, you need to do something to cool the piston down and you will know that a head temp of 390= danger zone.
the CHT thing is really only useful as a comparison tool, to tell you if something has gone wrong or to compare from one similar setup to another.