RBad,
If you are gonna have to punch out the cyl to the next few Thousanth's the biggest performance gain will probably be the fresh top end. If you are going to a 110 or so you would certainly feel a difference along with possibly a carb change. Moving up to the next oversize from stock may require a jetting change, but your carb etc should be fine.
Does your cyl have a steel liner or is it nikasil plated? only reason I ask is there is quite a significant cost getting a cyl bored and replated as opposed to bored and fitted with a liner.
There is a member here whose username is "Sapper".
He has lots of expierience with the 65 to 100cc engines as he does all of his kids maintenance and engine work for their racing team. (MX)
Probably the best advice I can give you is to get in touch with Sapper, He's a great guy and willing to share his knowledge. If I had someone like that when I was younger and listened to, I could have saved years of frustration, money, and blown up stuff.
Some information you might get ready for him is what kind of riding the KX100 is for, how much maintenence do you do, what type of rider do you consider yourself (honestly now) and of course how much money can you afford to spend.
Tuck\o/