Motorcycle Repair: Yamaha XS400j Maxim with Uneven Cylinder Temperature and Exhaust, rich fuel mixture, yamaha xs400

Question
Hey, I am restoring a yamaha xs400 that sat for 12 years to working condition.  And, it's working.  Mostly it just required some crazy carb cleaning and derusting of the gas tank. Actually, the bike works pretty well. The problems are fairly subtle but as I am planning on taking the bike on a 3000 mile trip I figure that subtle can turn into really bad really quickly.

There are two main problems. The first is that the bike hunts and surges between idle and 1/4 throttle.  Then it acts funny decelerating in this area too.  It is also slightly harder to start when it is cold.  Finally, i can hear an unusual, somewhat irregularly timed, pinging sound from the engine that seems to go away as the throttle is opened. The choke improves things somewhat but it still has the problem with uneven throttle response. I assume this is from a lean (or rich) fuel mixture but I tried the tape over the air vent (and removing the air filter) but it didn't improve.  

What I think is complicating the issue is that the cylinders are running unevenly, which I assume is due to a carb issue (uneven synchronization or differently turned pilot screws).  The right cylinder runs really hot after a 1 hour ride in city driving conditions at relatively cool ambient air temperature.  So hot that it will evaporate water when placed on the heatsink around the cylinder (side question: How hot should engines run?). The exhaust, however, smells good and doesn't seem to be backfiring.

The left cylinder runs substantially cooler. The exhaust however smells of raw fuel.

So is one running lean and one running rich or is one ok and the other out of adjustment? Is the one cylinder overheating? or perhaps is the other one not running hot enough?  thanks so much, galen.

Answer
Hi Galen,

This is somewhat out of my league, however, my best guess is the left cyl runs much cooler due to excess fuel , hence the raw fuel smell..
The right when leaned out too much WILL in fact run much hotter.

Make sure all of your jetting is correct for the application, the carbs are properly synced, and also make sure the seals between the boots and the engine are sealed. this will also cause a lean condition on the right cyl. if its taking on too much air..

Hope this helps!

~Mark D. Panka