I had a problem once with my front cylinder going out, but hopefully my problem is not yours. First how many miles are on you bike? and what year?. When you get back home from your rear cylinder cutting out what do your plugs look like (shiny black, fluffy black, really white, Wet??? ) Your plugs can tell you a lot about how your motor is running.
The rubber tip on your needle valve (if you have not already checked it) may be worn and allowing too much fuel to come in. Too much can choke out a cylinder too. Have you checked all vacuum lines to be sure you are not getting air rather than fuel. Let me know that and I may be able to guide you in a better direction