2011 International 9900 w/ISX 500 - unexplained missing at idle

Hi guys/girls, I have a freshly rebuilt ISX CM871 with about 10K miles on it now. My problem which has been going on, even before the rebuild is: When I high idle the engine using the cruise/idle switch, the engine will develop a pronounced miss, that seems to build to a peak then smooth out and start over again. Funny thing is, when I turn off the idle switch and hold the same rpm with my foot, the miss is nowhere as bad, but you can still hear/feel it. Has anyone had this issue, and how to go about checking without throwing parts at it?
The truck otherwise has great power and no detectable missing while driving.

 

P.S. The other issue I forgot to mention is: The high idle began to "kick out" at any RPM above 1050 on it's own, after about 5 mins.

 

Hi Heavyd. I thought with the rebuild, the missing would stop (new injectors/head/cams/rockers) with entire bottom end redone. Took it back for them to investigate the missing. They checked with Insite and said they couldn't find source of miss, thinking it might be electrical, as it is much more pronounced with the high idle activated. Even when the high idle kicks out over 1050rpm, no codes are shown.

 

Maybe I should try another repair shop? Starting to lose faith in their abilities to diagnose problems.