I actually doubt the rear is running rich, it is more likely that you have an intake or exhaust leak at the front and someone had jetted the bike rich to compensate for this. Since the single carb feeds both cylinders, an intake leak on one cylinder will make that one lean, causing the opposite cylinder to appear rich.
To check for leaks, REMOVE the air cleaner, leaving it on will give false readings. Let the bike warm up, then using a can of brake cleaner witha straw, point the straw directly at the intake flanges where they meet the head and at the rubber seal between the carb and manifold. ANY change in idle means they are leaking and need replaced. Replace ALL seals. Also do this check on the exhaust, at the heads and if you have mufflers or cross-over pipes, check those joints as well. Exhaust leaks will also cause a lean condition.
STOCK carb jetting should be 45 pilot jet, 175-185 main jet, 2 1/2 turns out on the idle mix screw.
If you have a different carb, let me know so I can give you and idea on jetting.
EDIT...Sleepy, below me has a valid idea, he is referring to the direction that the accelerator pump is squirting fuel into the manifold. This is usually not a problem on a stock cv carb that your bike came with originally ( the nozzle is TIGHTLY pressed into the carb and aimed at the factory), or an S&S as they use a fan spray instead of a stream (however, the nozzle do get clogged and can spray in any direction or even shoot a stream instead of a spray)...Mikuni carbs use an adjustable nozzle that can over time turn slightly, you can GENTLY use a small pair of needle-nose pliers to aim the nozzle to hit the slide needle which is centered in the throat.
Another possiblity is having a weak plug wire not giving full voltage and fire at the plug. Always replace plug wires ever 3-5 years or 25k miles.