Both the stock Hitachi 306 and the Weber 32/36 are "mechanical secondary" carbs.

Sure you can "jet" the stock Hitachi carb ... it will help a little to fatten up the air/fuel ratio. Especially as you've modified the exhaust system so much, it will make some difference. However, this carb is purposely on the small side for fuel economy and smooth throttle response.

For performance (if you rev over 4,000 rpm regularly ...) use a 32/36 or another carb that you are familiar with. For more info and ideas, See the Tech Section article Weber 32/36 Carburetor.