I have been told you can remove the baffles from your mufflers which will give a better sound. what affect will this have on the efi system? should i have the computer reprogramed? I have a 2004 fat boy with efi.

 

Your openening of huge can of worms here, and its already been done.
I'm of the opinion that as long as you don't change you intake, your fine. I have been so far.
Did you do a search for "drilled Baffles"? Lots of info here already.

 

If you pull your baffles you will lose needed back pressure. You will need to re tune your efi because you will change your AFR by allowing more air flow through your bike.

 

Any change you make to your exhaust or intake will change the amount of air running through your engine. If you change the amount of air, you should change the amount of fuel - and fuel is controlled by the computer. Will it run without a tune, yes. Will it run well, maybe. Will it be perfect, no (but then what is ever perfect).