Hello V-Twin. I just installed the upgraded breather and V and Hines exhaust, then had the S2Cams dealer installed.
The engine performed perfectly through 1 tank of fuel until I installed the S2C and then I got all kinds of issues. Did a search last evening and you described my issues with absolute perfection.
In my case I expected the issue to be caused by the air cleaner because I designed and built it. To test I first did a ride without the breather outer cover and without the K7N air filter. It wasn't as bad.
Next I installed the outer breather cover and ran without the K&N filter. Still an issue in fact a little worse.
I placed my hand inside the air box while riding (no filter) and I felt the crank case ventilation pushing a rapid pulse of a lot of hot air. That air was hot and was being pulled right into the throttle body intake and because the engine lopes at idle it was a pulse and I believe the on and off hot air was confusing the sensors and they were trying to compensate but resulted in the loping and jerking rhythm. As a final test I pulled the crank case tube of the rocker cover and taped it up with black electrical tape, then installed the K&N and did the test ride. My issues are gone.
The engine ran perfect, no 2000-2100 rpm issues of loping and jerking and the idle works fine at 750 rpm. There's is a little irregular shake but that's to be expected with any upgraded cam.
My issue is caused by the crankcase ventilation being too close to the throttle body intake. I'll need to install an inner deflector cover to route it to fresh cool air on the inside of the breather backer plate. Once the hot air and cold air mix there shouldn't be a problem. Or I can vent to the atmosphere directly using a filter.
You might want to check your location of the Crank case ventilation being too close to the throttle body intake.
IHTH John in Red Deer