1990-2004 Cylindwer height stock 142.2mm

[Sandblaster]

From the bottom of the cylinder to the deck a stock KX500 cylinder 90-04 should be 142.2mm.
If yours is less, then it has been decked or material has been removed from the bottom.

Typical dimension while the piston is a TDC, the height between the outer edge of the piston to the deck is approximately .010" if a .020" base gasket was used.