You have 2008 model, so it has the old style Touring exhaust system (unless you changed the headpipes out for something like Rinehart, etc.). Those exhaust systems route most of the exhaust to the right side muffler in normal riding; you don't get equal flow from both sides. So that accounts for feeling less flow and less heat if you put your hands behind the two mufflers with the engine running. As for the amount of carbon, same answer. The left muffler shouldn't look as clean as a brand new one in the box, but there will be a visual difference in most cases.
If you did a true leakdown test, you should already have a good idea of where any excessive leakage could be coming from. With a particular cylinder pressurized, you can listen at the intake, the exhaust, and the crankcase for signs of air leakage. This can help narrow it down to rings/pistons/cylinder walls, or valve related leakage (exhaust valve leakage will be heard more in the exhaust, intake valve leakage in the intake tract).
Jerry