Unplugging it will basically make it so the ignition box doesn't know what throttle position it's at. We don't know what the exact changes in the ignition box are based on throttle position because it's all proprietary information, but it does alter it. The side effect for me, was my bike ran better - and that was 7k miles ago
I'm not saying it's the right thing to do, but it worked for me. Maybe my TPS is bad (it did measure up to spec based on the instructions in the manual though), but I'm not going to shell out a ton of money for another one. For me, it was night and day after unplugging it. I even took my bike in for a recall, and I knew right off the bat that they had plugged it back in.
Assuming my TPS isn't bad, my theory is that these bikes weren't really designed in mind for cruising the streets at a steady speed. I'm thinking that at a certain engine speed, we might be hitting a part of the ignition map where it jumps from one map setting to another (and back and forth). You'd probably never feel or encounter this on dirt.
Anyway, JD recommended it, and I trust him. or, it could be some other problem completely! :-D