I had similar problems as you with my 96 360 E. As Patman stated, the earlier cylinders were stamped with a 1. These cylinders were of the higher compression and are difficult to jet. James dean has provided the cheapest way to correct the jetting problems. I also did the Rad valve, FMF exhaust, and reed spacer thing on my 360. I was able to get it to idle and not foul plugs with a very similar jetting set up as James Deans describes. If you are using the stock exhaust, when was the last time the packing was replaced? If it is running as rich as you desribed and it's 4 yrs old, the packing may be saturated with spooge. That will impact performance as well. When you get this thing right and get a clean running bike, you will be smiling from ear to ear. Gobs and gobs of low end billy goat torque that will rev to the moon. You wont be asking, "how fast is this thing" but more on the lines of " I hope I have enough room to stop this thing!!" I'm smiling right now thinking about those fire road drag races!! Good luck.
Rick
99 300 EXC
96 360 EXC Memories