For what purpose(s) is the motor to be drilled?
What type of Yam two stroke? Carburetted? HPDI? EFI?
Doesn't it have exhaust reliefs on it? Or are you trying to.modify the exhaust because you think it will be faster?
With lots of noise it will be faster for sure.
Just start drilling until you get that sweet exhaust note that you desire!..... Great Idea!!!