Sorry for the slow reply I'm working pretty hard these days.
I agree with Dean, the Team Green tips are a great baseline. The specs are the result of a lot of field data gnerated by a thousand support riders.
People ask me all the time what to do with the KX/RM100. The cylinder is a fairly rough casting with many flaws that can be smoothed-down and rescaled for the 99cc displacement. The basic cylinder casting is from the KX85, just punched out bigger. Because the ports enter the cylinder at angles, when the bore is increased the port heights fall and retard in timing with a loss of overall duration. Overbores don't work on the KX100 because of the exhaust port outlet size. Crankshaft stroking (1.5mm off-set) works very well. Thats what the majority of Team Green riders are doing to their bikes for AMA and NMA championship races this year. However next year the participants of the AMA Amateur Nationals at Loretta Lynn's won't be allowed to alter the bore or stroke on their engines.
The best bang for the buck is porting to Team Green specs. That will run between $100-200 on the porting market. I'm real backed-up with work and probably won't be faster than 2.5 weeks all summer long. Two other companies I'd recommend are Boyeson Precision Porting in New Tripoli PA., and Pro Action in Beaver Falls PA.
Good luck, Eric