I listed the same problem on 4/08/01. I didn't explain it as well as you have though. I have my mufflers drilled like "BuzzyDBiker" and I re adjusted my pilot jets and it disappeared for a short time and came back. I shimmed my metering rods with a #4 washer and the sputter is gone but it snap crackle pops when I coast down a grade. The same thing happens when I forget and leave the choke on. I guess I am going to have to up my pilot jets by one size to #45's. Heck I may just re do all the jets??? This bike needs a little more umph anyway. This sputtering crap has aggrevated me to the point that I have spoken with a couple of Honda mechanics, and they both told me it is normal for this bike as long as it doesn't do it consistently.
I am going to keep working at it till I or someone else figures something out.
JCR