2-2 is the scientificly correct way to go. the crank configuration governs this. 180 degree crank, 2-2. sometimes the old mac pipes come onto ebay. or call tom @ delux works honda in california. they have a web site. he'll make you up a pipe that wont be perfectly tuned for max power, but it'll work just fine. 2-1. or you can goto ricepaddymotorcycles.com. they have stainless 2-2 pipes. i think the tuned length for optimum power is about 13" with 17/8" pipe/ but it gives you a really short crap assed pipe.
the drilling most definitely can affect structural integrity. on the clutch plate cover i think youd have to remove alot of it. its really only a cover. the problem with drilling the brake hub is as you said. water will get in there and rust things up. so it takes more maintainance. most people only drill about a 3/4" hole directly in the center of the webbing. ive never really heard of the 350 hubs cracking. more the t500's etc. ive seen them cave in too.
jc
the drilling most definitely can affect structural integrity. on the clutch plate cover i think youd have to remove alot of it. its really only a cover. the problem with drilling the brake hub is as you said. water will get in there and rust things up. so it takes more maintainance. most people only drill about a 3/4" hole directly in the center of the webbing. ive never really heard of the 350 hubs cracking. more the t500's etc. ive seen them cave in too.
jc