Motorcycle Repair: sportster cylinder fouling, combustion chamber, rear cylinder

Question
i bought a 92' 1200cc sporty.it had sampson long shot exhaust and 98' or newer heads. i took the baffles out of the exhaust. after about 300 miles, the rear cylinder was loading up with solid black carbon. i changed plugs and then 30 miles later the same thing. i took it to the shop and my mech. thought maybe it needed rejetted. he checked the bike out and said that wasn't the problem.then he checked the coil and plug wires. they checked out good.so he decicided he wanted to look inside the cylinder.he took the heads off and found minor scarring on the rear cylinder wall. the front cylinder was clean.he suggested honing the cylinder and installing new pistons. i let him do the work. after i got my bike back he told to ride it like it was new, meaning a break in period.after 350 miles the rear plug loaded up again. when i told the mech. he couldn't believe it was doing it.now that the rains are coming to oregon the bike is going back to the shop. the mech. said he couldn't think of anything that would cause a single cylinder foul. he's going to take the heads off again and see what he can see. i'm wondering if you have any reasons on what could cause this problem.

Answer
The only thing that can cause one cylinder the foul is either oil is getting into the combustion chamber or the coil is and plug wires are bad.
Even though he checked the coil and plug wires here is a test you can do. Swap the wires in the holes on the coil. If the other cylinder starts getting fouled then you found the problem. Your best bet would be to use new wires. Your coil can test fine cold, but be bad when it gets hot.
The other place you can be getting oil is from a leaking valve guide. You never said if he checked these.
Good luck and happy riding
Mike