Motorcycle Repair: rear cyclinder very lean, dyno tuner, mobile dyno

Question
I'am a small harley repair shop, and also a mobile dyno tuner. A customer bought me bike after having a jet kit installed at another shop.  Wanting it tuned on the dyno saying the bike ran bad on the top side (3,500 to red line).  After making a few jet changes and getting the AFR readings to 12.5 (with the sniffer in the front exhaust).  Bike still ran badly on the top side.  Thinking it might be an ingtion problem changed plugs, plug wires, coil, and computer.  Still ran very badly.  Then put the sniffer in the rear exhaust.  When the the bike gets to 3,500 the AFR goes though the roof.  The rear cylinder goes way lean in the high rpm. What might be causing this problem?
Bike is a 2003 softail, vance and hines long shots, with screamin eagle air cleaner.  Have also changed intaked seals.

Answer
Since the bike only runs on one carb and the fuel is split between two cylinders and you have only one cylinder lean then you need to look at a intake leak, exhaust leak or a burned valve.
I would do a compression test and a leak down test on both cylinders
Good luck and happy riding
Mike