Orderofsion:
I have flat top piston too and i guess that all kx500 have it.
Something what you could to do with your cylinder:
Raise exhaust to about 195deg, side exhaust 2-3deg more. Don't make exhaust duct bigger, only port. Maybe last 2mm raise quite steep, only about 10mm to duct. This help keeping gas in speed.
Raise main and second tranfers so that when main exhaust open to main transfers open is about 32 degrees. (32 is very very old fine starting point.) Less degrees (higher transfers) mean more rideable motor and more deg. more hit power (more dyno power.
) This depend very much of your pipe and your personal will. Raise boost transfer about 1mm less than main and second.
You have 2 choice:
1. Raise all ports, or
2. raise cylinder to get boost transfer or port which need less raising ok degrees. Make spacing plate of aluminium or so and use paper gasket both side. Remember that paper goes thinner in use. Raise all other ports.
If you select 2, then you have 2 choice:
1. Shave top of cyl. same mm what you raised cyl, or more to get squish in order.
2. Cut gasket level of cylinder head so you get squish in order. You cut nothing center of head, only gasket level. Then squish and whole combustion camber can drop to cylinder. I know that some of WC RR125/250cc-team use this. It's nice when your motor knocking, so your's cylinder top not ruined.
Then you must make combustion chamber back to bigger. How much depend of fuel.
I try to put Excel-attach (size 29kt) to this message. I change xls-extension to txt. Change it back to KX500std-86 eng.xls. With those Excel you can plan degrees and compression ratio.
Doordie: Would you check my writing again?