Jeff,
You could try the bike with straight through pipes to see if it is too loud. If it is, it's not a big problem to alter the pipes some time later. The welding/machining will be on the part that is hidden inside the waffle box, so wont affect the appearance of the bike.
The original pipes were blanked with washer with a 5/16" hole. On the inboard side, the pipe has 7 slots x 3/32" wide going about half way round the pipe - the first slot is 16mm from the end and the rest are pitched at 15mm centres. When milling the slots, I have found it pays to cut the slots prior to blanking the end - then a strip of 1 1/4" wide steel can be inserted into the pipe to support it whilst it's clamped in the milling vice.
Regards,
Eddie.