2004 Honda Shadow VLX 600 If I drill out the rear baffles on stock exhaust with a hole saw will bike still run good or have to put in jet kit make another modification?

Removing the baffles from your stock exhaust will reduce the backpressure in the system and allow the engine to breathe more freely, which will likely result in a slight increase in power and a louder exhaust note. However, it is possible that this could also lead to some fuel delivery issues, such as a lean condition, which could cause the engine to run poorly or even damage it.

To avoid this, you may want to consider installing a jet kit, which will change the size of the jets in your carburetor and allow more fuel to be delivered to the engine. You may also need to adjust the air/fuel mixture screw to get the bike running properly.

Alternatively, you could have a custom exhaust system made that is designed for your specific bike and will not cause any fuel delivery problems.

It's important to weigh the potential benefits and risks of modifying your exhaust system before you make a decision, and it is always a good idea to consult with a motorcycle mechanic or exhaust specialist if you are not sure what you are doing.