Hey all,

It has been a long time since I posted to this forum - I gave up on ever getting my GS to run properly.  Recently I recommitted to finishing this bike since everything is ready to go except for this damn dead cylinder.  I have a few questions at this point, perhaps you guys can help me figure this stuff out.

I discovered that the brown wire leading from the signal generator to the CDI has an open in it.  No continuity there.  Before I discovered this I had already verified several times that both spark plugs were firing.  Odd that both plugs would spark when one sensor had a disconnected wire.  Frustrating that connecting the wire didn't bring the cylinder back to life.
1. What are the sparks supposed to look like?  The ones I observed were tiny and blue.
2. What is up with both spark plugs firing when one of the wires to one of the sensors was disconnected?  The sparks are NOT supposed to be timed together, right?? If they sparked at the same time one cylinder would be filling with fuel at the time the other cylinder is supposed to be combusting.  Do I have this wrong?
3. Could having that brown wire disconnected have fried the CDI?

The engine has a real hard time starting up.  One time I decided to cover the intake of the dead cylinder with my fingers and discovered that the engine will spring to life (on one cyl).  The better the seal I create with my fingers the quicker it starts, if I get it to pull a decent vacuum on my fingers it will start in a snap.
4. What kind of problem could this indicate?  I am having a hard time imagining how this would make the engine start easier.

I have a very long list of things I have checked and I have a short list of things remaining to check including check valve clearance, replace jets, and spray starter fluid into the dead cyl.  If those things don't bring the cyl back to life I guess I will swap out the CDI (again) and the signal generator.  After that I will be thoroughly stumped.  So far I have bypassed the frame mounted fuel rooster, checked compression (135 psi both cyls, cold dry and with 5 revolutions), checked cam timing, swapped plugs wires and coils back and forth, checked for vacuum leaks, checked continuity of all wires, checked resistance of signal generator sensors, and more that I am not remembering at this moment.

Covering the intake makes it run.  That's an old tuners trick to check what happens when you richen the mixture.  Blocking the air leads to more fuel being sucked relatively. 
Have you cleaned out the carbs?  Sounds like it had been sitting a long time.  That can gum up the carbs. Your pilot jets might be clogged.

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Cool, that kind of makes sense to me.  I paid for a new set of jets from Buddha so I'm looking forward to trying them out.

I have had the carbs of a few times and the jets look clean to me, perhaps they are the wrong size?  I wonder if there could be something wrong with the jets that isn't obvious or visible.  If they were scratched during cleaning or if they have surface defects could that stop fuel from flowing?

I'll pull the carbs again and inspect the pilot jets and wait for the new jets to come in.

So I pulled the carbs and checked out the jets, the pilot jet did seem to be clogged.  I used a bristle from a brass wire brush to clear it out.  I put it all back together and started it up, again the bike started up right away when blocking the air to the dead cylinder.

I wonder if blocking the air to the good cylinder will also help with starting.....

While I had the carbs open I realized that I do not know what one of the passages is for.  What is the tall skinny one that lives inside the float bowl plastic thingy?  I poked inside it with a piece of wire and fished around inside, it might have been clogged, I think I knocked some crud loose in it...

Should I soak these carbs in a cleaning fluid?  A friend thinks coke would be effective in eating away the gunk.

Lucas, there are many ways to clean carbs. Soaking them in cola "could" work..... but I wouldn't try it unless it was an absolute last resort. Cola is acidic, which would eat away at some grime but it can eat away at aluminum as well. Not to mention you would need to wash ALL the cola residue out of the carbs.

I'd recommend boiling them - do it outside in a pot that you never plan on eating from again. And try to take the carbs apart as much as possible.