Left cylinder not firing

[Egaeus]

Okay, I'm having a problem with my 99 only running on one cylinder.  The left cylinder will kick in only at relatively high RPMs.  I also can't get my carbs to balance.  The right will increase vacuum with very slightly increased RPM much more than the left.  This has been occurring both before and after rejetting + K&N drop-in filter. 

The stats:
Pilot Jets: 40
Main Jets: 127.5
air mixture: ~3 1/6 turns out
idle: currently about 1750
Compression: Left: 980 kPa Right: 1000 kPa
Spark plug inspection (after maybe 1 hour of runtime):
Right: insulator has a nice tan color
Left: insulator has a dark brown film, looks like cooked-on oil

I heard the valves, so I checked the valve clearance.  The left intake clearance is nonexistent.  I can't put the 0.015 mm feeler (smallest I have) in.  I think it may be ever so slightly open all of the time.  I will have to wait until at least Tuesday to adjust the valves due to availability of parts.  Do you think this is the problem?  I'm thinking maybe it is, because at higher RPMs, a leak would allow less air through, causing the cylinder to have higher compression and fire better.  Also, I get a bit of backfiring out of the carbs occasionally.  However, I thought I'd put this to the forum, since you're much more experienced at this than I am.

EDIT: It's the 0.038mm feeler, which is 0.0015 *inches*.  I think it may have no clearance because the cam lobe shows the slightest signs of wear all around.

Thanks!

[starwalt]

Ah yes, LCDS, "Left Cylinder Dysfunction Syndrome."

Kerry had a lengthy post of this and a few others have reported such a thing. The source of the problem is usually electrical in nature, though not a given. Enter "left cylinder" in the [Search for] box and "Kerry" in the [by user] box.

Check to make sure the auxillary ground, the small wire coming off the battery that feeds into the wiring harness, is connected or non-corroded. Below is the connection as near the negative terminal of the battery. (Click the picture to enlarge)


Another view of the same from a different angle. My battery box on the rebuild is red. (Click the picture to enlarge)


Another possible poor connection is the engine ground point. The large negative battery cable is terminated on the bottom of the engine. Make sure that one is clean and tight also.

After reading the search and checking those things, let us know.

[Egaeus]

I forgot to mention that I have a good spark from what I can tell.  I've grounded the plug on the engine and it's sparking very well.  Side by side, I see no difference between the two plugs.  I have spark, I have compression (though slightly less than the right), and I have air, of course.
 
I tested the "bad petcock diaphram" theory by putting it on PRI and pinching off the vacuum line from the left carb.  No change. 

I checked the float height, and the fuel level is slightly high on the left.  Instead of it being at the seal, it's about 3/16 of an inch above it. 

The aux ground is connected, and is clear of any corrosion.  I didn't check the main ground, but a bad ground should affect both plugs equally. 

I'm going to try and start it on left cylinder only tomorrow.  I bought a spark tester so that I can properly ground the right plug wire and not burn anything out. 

[hayabusafiend]

Your valve clearance is below tolearance.  Adjust the valves and balance the carbs.

[Egaeus]

Your valve clearance is below tolearance.  Adjust the valves and balance the carbs.

That's definitely in the plan, though I won't be able to get shims until Tuesday, if the stealer even has them in stock at all.

[Egaeus]

Veeeeery iiiiiinteresting.  So I did go ahead and start it on just the left cylinder using the spark tester on the right so that I wouldn't burn up any ignition components.  I couldn't get it to start without giving it quite a bit of throttle.  I turned the idle up and it ran fine.  So I adjusted the carb synchronizer screw to increase the idle speed on the left, and by going back and forth between the two cylinders, I got the engine to run on either cylinder at the same idle speed.  I then connected both cylinders, lowered the idle, and it seems to run fine.
 
However!  Now, when I attach the differential manometer (that I built with aquarium airline) to the carbs to see if the carbs are balanced, I get much more vacuum on the right cylinder than the left.  So much so that if I closed the adjusting valve all of the way, it would suck the water out of the manometer.  Balancing the carbs according to this causes the left cylinder to quit running. 

Any ideas?

Oh, and yes, I know I need to adjust the valves before I synch the carbs.