Not sure what else you've done but you might check a few of these ideas:
1. Compression Test. Make sure both cylinders are somewhat close in compression. You might have a bad valve or gasket.
2. Check for air leaks at the intake manifold to cylinder head connection. (Spray ChemTool B12 around the connection and see if the motor drops a cylinder).
3. Make sure the accelerator jet is spraying in the center of the intake manifold and not towards on cylinder (maybe the rear in your case).
4. Check the spark plug wires. You might want to get a new set.
5. Do you have a single coil or a dual fire coil? This could be an ignition problem.
6. What kind of ignition do you have? It could be heat related if this problem shows up after you've been ridding awhile.
I hope this can give you some ideas to check for. However, I'm sure you've already done some of these.
