I had a similar issue and it ended up being the battery. I took a volt meter to it and it showed proper voltage but when I took it to the dealership, they put it on a tester and the tester said replace. After it was replaced, it's been running great again. I changed the plugs prior to taking it and it helped a little but still felt like it was missing ever few rpm.
2005 - VTX 1800F - Silver
2008 - Shadow Aero 750