Front cylinder misfire at idle,then raise rpm's to 2000 area an it comes in an out popping thru exhaust.front cylinder cold to the touch when rear is hot, till it runs a couple of min. New plugs, good compression, tested spark with an hei plug fire tester.rejetted carbs with dynojet kit per there instructions. I fabricated rear cylinder pipe to come out of left side and added fishtale duals. Ran this way before I did any of these things. Bought bike with 900 miles on it. Clean gas and some gas additives put in. When it warms up it feels better,but when it acts up and your driving and give gas an it kicks in u'd better be hanging on or u'll !!

Check to make sure the carburetors are synchronized. If the rear carb is open more that the front it will create the problem. With the engine idling try slowing opening just the front carb. These motors run really lean from the factory. If even the air box cover is off they just won't run. Fatten up the jet a couple of size and it will make a big different. I would fatten up the jets to where you can rev the engine with the air filter off, remove the rubber in take tube (note how small the hole is in that tube) and or drill a couple of holes 1/2-3/4 inch on the inside of the air box by the front cylinder (not the out side cover) Install a high flow air filter. This helps out air flow a lot and helps performance. It will not affect gas mileage as you will us less throttle to go the same speed.

I am not sure if the bike is a 650 or 1100 but in either case it sounds like a fuel issue or and air leak. When the carbs were off for re-jetting did they get cleaned? The slow circuit controls to about 2000 rpm and it sounds similar to your problem.

The first thing to look at is the carb synchronization. If the front cylinder is lagging, it can give the same symptoms. I do not think that the exhaust is a factor because the front is cold when running.

Spray some WD 40 at all the intake manifold area when the bike is running and see if the idle changes. the idle will change and push some smoke out of the exhast if the intake is leaking.

If both of these check good I would pull the carbs back off and clean the slow circuits out completely. This is delicate work and shoud be done by and experienced tech.

If I can help some more just send message.

I hope that his helps. Steve

I have got a XVS650 1999, it was running fine, I put it in a garage for around 18mths, when I went to ride it, it would not start, new plugs, new battery, easy start, just backfire, cuts out & front cylinder runs cold. I have had the carb's off three times for cleaning, last time ultra sonic cleaned, carbs set up as per specs,
still the same, exhaust gas from back hot! front cold!