because of the machine shop bit, check your piston to make sure it is clearing the intake and exhaust ports correctly, if not correct it with gaskets.
for jetting, do plug chops and rejet accordingly. you may just be running too lean or too rich and thats whats causing your problems.
you don't have to open the intake if you open the exhaust, but like tim said, you really should.
are you running a 15mm intake? if not you arent using all that carb's potential. youre not going to see great performance improvements runnning a 15mm carb into a 12mm intake then a 12mm intake port.