Motorcycle Repair: Poor idle, rear cylinder pops, hard krome, rear cylinder

Question
Hello Mike
Thanks for your time and help, I have a 1998 fxd, no engine mods,I added a K&N filter, the carb was just cleaned and rejetted for Hard Krome 3in slip on ehaust. My problem , before and after the exhaust and jets were added, is that the motor will not idle well and the rear cylinder pops every few revolutions. I put my hand in front of the front exhaust and the pulses are consistant, the rear is irregular with surges or pops. The bike, when warmed up, runs well down the road, good power and no hesitation. At rest the motor wants to slowly die, like the carb is running too rich, I smell heavy exhaust, and I have to keep the rpm up to keep it from dieing. If I idle for more than a minute or two, when I take off it cuts out for a few seconds until the carb clears.
If I go for a ride and have to shut the engine off, like to fill up on gas, when I try to start the motor, no choke or throttle, I have to crank and crank to get it to fire and run, like it is flooded. It will then run like crap for a few hundred feet. The shop that I took it to for the carb work says that it is set up with as lean a jet as they could without it causing warmup issues. As it is now, the bike runs like total crap until I get a least 4 to 5 miles down the road, bucking, jumping, popping, backfiring thru the carb, I have to be VERY gentle with the gas when trying to get up to speed to avoid poor running until it is warm. This is after I let it sit warming up for at least 5 minutes before I even get on the road! It will idle with the enrichner pulled out, higher rpm, but it stays running. When cold, the engine will start easy with the enrichner out and a couple pumps on the gas.  Could this be an ignition/coil problem? I have changed plugs and wires with no change in symptoms. Your thoughts and ideas would be greatly appreciated!

Gerry

Answer
First I would test the coil to see if its going bad. If its ok then check your intake manifold for a leak. You can do this by letting the bike warm up and spray a little carb cleaner around the intake. If the idle goes up then you have a leak.
You stated that the shop put in leaner jets. When you added the filter and the exhaust, that should have made the bike run leaner already, so they would have had to richen it up to get it to run correct.
Good luck and happy riding
Mike