Jesse,
Before I got my Yosh slip on I did drilled out the baffles in my stocker. It made more sound, it was an improvement, but no improvement in the performance. Being able to hear the engine was good for me though, I like to know what's going on and with the stocker sometimes I actually could not hear the engine over the wind noise.
I suggest that you wait until you can get yourself a nice Yosh slip-on. No prejudice here, they are just the best (IMHO, no offense to anyone). A new slip on with a mid pipe will make a difference, even without re-jetting. When you re-jet (you will) things get to be really fun!
Steve