I have been doing this punch out for a umber of years on different bikes. This as with all mods the basic rule applies that what you do at one end you must balance on the other end.
When you drill out the muffler you are relieving back pressure, and leaning out the mixture .If not corrected it can over heat the engine. With the old Carb systems it was a simple matter of changing the needles , and plugs.
The lasyt bike I punched out was my VTX 1800 when I triked it out. They had increased the length of the pipes using the stock mufflers. This increased the back pressure making it run like crap, and dropping the MPG way down. I used a 1/2 inch drill with a 24 inch drill extension. I started off with a single 1/4 inch hole coming from each end. Then took it out for a ride.Then repeated it. Performance started to increase . Got it back up to where the performance and MPG where doing good , and sound did not rattle my neighbors windows. Plus I do not have any backfiring which indicates to lean of a mixture.
In short if you are going to do it take your time.