Just for kicks I went and measured a stock kawasaki and Cometic headgaskets, yep you guessed it, they measure 88 mm. The base gasket will be different between 86, 87, 88 and the 89-04 the newer motors have the 3 KIPS shafts whereas the older motors only have the 2, the cases are a bit different on the older motors as well in the KIPS area. The headgaskets are much larger and thicker on the older motors.
And as far as using Silicone for gaskets in the motor, I would'nt reccommend it, gasoline will dissolve most silicone, if you must use some sealer use something on the order of a copper coat or whatever the permatex hi-tack. I haven't bought a stock KX base gasket in quite some time, I would think they would be using the same material as Cometic since they do on the 125 and 250 base gaskets.