Welcome to the board! So, to run, an engine needs proper air/fuel mixture, compression, and ignition. My bike has run on three cylinders a couple of times since I've owned it.
The first time the bike had the problem, I fixed it by cleaning/rebuilding/balancing the carbs. The o-rings were past their prime and the idle air screws were all out of whack. Turning them all to 3 turns out was the best setting for them. Went back and forth between idle screw adjustments and balancing a few times but it was all worth it as the bike idled very nicely after that.
Were your carbs balanced after the rebuild? All the ports on the top of the carbs plugged? You can make a cheap manometer to balance the carbs using a length of tubing and some colored water. I think I spent less than 5 bucks on the tubing. You can find that tutorial here.
http://www.powerchutes.com/manometer.aspDo you have an inline fuel filter between the tank and carbs (in addition to the tank filter)? Doesn't take long for a tiny piece of crud to work its way from a rusty tank and into those clean carbs.
The second time I dropped a cylinder happened just a few weeks ago. After crapping out on me at a stoplight, the bike wouldn't run at less than 3k rpm. Touching the header pipes told me right away which cylinder was down a year and a half ago. It didn't tell me anything this time, because at that rpm, the miss seemed to be intermittent, and all pipes got hot pretty quick. I then checked spark at each cylinder with one of these.
http://www.harborfreight.com/cpi/ctaf/displayitem.taf?Itemnumber=36258It'll let the bike continue to run normally while telling you if that plug is getting a spark. All cylinders were getting a spark, so I pulled the plugs. All but cylinder 1 looked fine. That plug was a little wet. I then reinstalled the plugs and plug wires. Fired it up and individually pulled each plug boot off its plug. Only cylinder 1 showed no change. All the other plug wire disconnects dropped the rpms dramatically and turned the bike into a twin. So cylinder 1 was now my main suspect.
I didn't suspect compression (but didn't rule it out), because the bike was running fine one minute and just died on me the next. Rings wear slower than that, and I would have probably heard a valve snapping! ;)
Soooo, off came the carbs. Verified the air screws were all at the same setting (they were all still 3 turns out). Tore them all apart and cleaned them. No obvious problem inside. Reassembled and reinstalled, but the bike was still having problems.
I suspected that the cylinder 1 coil was flaky, so I re-crimped and soldered the primary connectors and measured the primary and secondary coil resistance while I was there. All measurements came up good with my meter. Refired, but the bike still ran on three. I then swapped out the coil with a spare I had and it fired up and ran great! Swapping around some spare plug wires and the bad coil proved that the problem was with the coil.
I suspect that even though the coil resistance measured fine on my handheld fluke meter, it would fail a high voltage resistance (Hi-Pot) test. Which implies the primary and secondary transformer wires inside the coil assy are shorting out to each other when powered up.
So, hope this helps a little with the troubleshooting. Good luck and let us know how it turns out!
Russ