Need some brainstorming

[chiphead]

If you have access to an inductive pick up timing light, when the bike is "running poorly" hook it up to each plug lead and watch the light to see if you can detect a variance in the pulsing of the timing light on each cylinder. Repeat when the bike is running well. This will help you isolate whether or not it is an ignition issue.

[KEITH KRAUSE]

When I mentioned checking/cleaning the plug cap connections, I meant to unscrew the caps and inspect the end of the leads. If the copper has any corrosion/green color to it, you can usually just snip off a 1/2" and give the lead a "new" connection.
Did you inherit this problem or did it run well before and then it started doing this? I'm trying to figure out if there could be PO jetting changes or whatever that could cause a weak spark/no spark condition or a part has just started failing.
This bike is stock intake and exhaust? Stock jetting?
What colors are all four plugs after some general riding around town?
If you start it up and warm it up, what happens if you then disconnect each plug lead at a time? Turn bike off between each disconnect to avoid a shock. Re-start. Any effect? I'm trying to see if you're already running on only 3 cylinders until you go out and ride it harder. A weak firing cylinder will many times let the pipe/that cylinder get hot but it's still not allowing constant/good combustion.
What plugs are you running?
Are all four mixture screws set approx' the same?
I'm ASSUMING the carbs are clean and adjusted well, per your post. That would leave only the jetting suspect if this is carb related. Trying to narrow this down.

[t3rmin]

Here's another vote for plug caps. Had similar problems myself, and replacing the caps fixed it right up. It would drop a cylinder or two when warm, but not always when warm -- it was somewhat random. Drove me crazy for a while trying to figure it out. New NGK boots are cheap at z1enterprises.com and they look nicer, too.

There is a resistance test you can do (GS caps are "resistor" caps), but I first found out by handling them while the bike was running and getting a shock, so you can give that a try if you're brave. ;-)

Also check the voltage at the coils. This old wiring often leaves you with less than full voltage by the time it gets all the way to the coils. Probably wouldn't cause the problem you're describing, but something to check nonetheless. You want as close to full 12v as possible.

[kungpaodog]

I'm 99% sure that it's stock jetting, maybe I'll pull them again and check, but it seems to come and go too sharply to be jetting.
Intake and exhaust are stock.
The plugs are Autolite.
The color of them is all a good light brown, but I suspect that cylinder 3 may be firing intermitently since a brand new plug seemed to show less color than the other 3, but it may be just tuned better than the others since it looked like the perfect plug color.
The mixture screws are all set at about 2 1/8 turns out (I'm in Colorado, so this makes sense to me to adjust for elevation, right?).
I think I inherited the problem because it was non-running when I got it, but it ran with some fresh gas (poorly) before I even cleaned the carbs.

I checked the coils last night, and they look to be fine visually. All the connectors are in great shape, there are no cracks on the bodies. When I pull the caps off and put in plugs and run the bike, all 4 plugs look to fire well. AAAGHHHH!

There's a set of used coils and a R/R on ebay right now that I could pick up for $25 and $30, respectively. I don't want to just throw parts at it, but would it be worth a few bucks to try new coils?
Thanks for the time and concern, guys!

[DickV]

I suggest you take the coils to a shop that has a coil tester and have them checked under load. The coil resistance test can be within or near spec but when there is the high voltage generated the windings can short due to bad insulation on the secondary windings. I had this happen and new OEM coils worked magic! Good luck, Dick V

[KEITH KRAUSE]

If the plugs are a light brown on the ceramic around the center electrode, that's generally a good sign that the jetting is good and the spark is adequate. You can still have an intermittent problem that would likely be a poor electrical connection. Higher rpm's usually helps a poor connection, at least it seems to perform better.
I tend to think it's electrical. Specifically, a poor connection.

[chef1366]

Get some NGK plugs.

[kungpaodog]

Thanks Chef, Keith, Chip, Dick.
I took a few days away from the bike to go snowboarding, so here I am again, still looking for new ways to confuse myself...

I chopped about .25" off of the plug leads and put the caps back, on, and the plug caps look to be in great shape. There was just a little bit of corrosion on the wire ends, but not enough to get me worried.

The voltage at the orange wires going into the coils was 11.5 on one side, and 9.5 on the other (the 1/3 coil). Then I disconnected what I'm pretty sure is the R/R connector and the voltage went up to 11.5 on the 1/3 coil. Is this right?

Then I put a timing light on her, and while the advance works perfectly, the 1/3 coil seems to be very intermitent at higher (over 4000) rpms. The 2/4 coil seems to work well at most rpms, at least my timing light fires a lot more off of the 2/4 coil than it does the 1/3 coil.

To top off the confusion I checked the voltage again after I did the timing check, and voltage was 11.5 at the positive leads going in to both coils.

Do I need to tear into my wiring and/or do a relay bypass to the coils? The wiring looks very clean all around.

Do I need a new R/R or do I need new coils? I'm leaning towards new coils, but wanted to ask first. And I also wanted to know where I should order them from. Plug your buddies business here!

Thanks for all the help guys, I know this is a lot of info to sift through.

[KEITH KRAUSE]

Just to avoid troubleshooting confusion, one coil fires 1/4 and the other 2/3.
The voltage to your coils should be higher. Clean connections everywhere are a must, as is a correctly charged battery.
Check the coils secondary (plug cap to plug cap) resistance. Generally, 31 to 33 ohms resistance is good, but I'm not sure about your specific model. Check the primary resistance, it should be between 3 and 5 ohms.
Your ignitor controls power to the coils. It could be failing, but I'm hesitant to advise about testing it because I don't consider myself experienced enough with them. You can short out/damage things if you test them incorrectly. The only info I have about testing the ignitor is when using a specific Suzuki tester. I can post that info if you want it, but I don't know how the use of a different tester you may have changes the procedure.
You said your signal generator passed its test.
Your test light showing intermittent spark at one coil certainly suggests a problem.
Coils generally fail more often than ignitors. Unless you can make thorough tests of the ignitor, I'd probably look at replacing the coil that was part of the intermittent sparking. Of course, I'd make sure that each and every connection is solid/clean first.