I had a 20psi difference between my cylinders about 6 mos ago after a dune trip come to find out the base gasket was leaking on one side. So I rebuilt it with new rings and made sure to use 1211 gasket sealer on every gasket and re-checked...they were both reading dead on after that.
Even though they were 20 psi off, my bike still ran strong..I just happened to check compression for the hell of it and found the problem.
So I guess what I'm getting at is that you do need to address the difference in compression but I don't believe that is making your bike bog at WOT unless it's an airleak. What temp does your bike run at? If I were a betting man, I would say you have a leak somewhere causing one of your banks to run lean and hot hence crappy at WOT.
DO a leak down test and make sure it holds 6psi of air for 6 minutes and if it doesn't then spray around the gaskets with soapy water and look for bubbles, you will find your leak. If you don't have a tester, you can make one from parts at a local ace hardware for about 20 bucks. If you do a search on here, somebody did a write up on how to build one.
By the way, with stock cylinders, aftermarket pipes and filter...you should be running between a 280-320 main.
Hope this helps....good luck!