One way to troubleshoot a possible EGR sticking is to drive it on level roadway at a constant speed (basically a no-load cruise). If you experience skipping, stop and pull the vaccum hose and plug it, then repeat the drive. If the repeat cruise has no skipping, your EGR is probably sticking and either needs cleaning or replacing (if you intend on having it functional).
If you're in a no smog test location, pulling the vaccum hose and plugging it won't cause any issues - so long as the EGR valve is CLOSED. You can use a screwdriver to help if it's stuck in a partially open position. If you have carbon buildup on it, you'd be better off to pull it and clean the debris off of it, re-install, THEN plug the hose.
Personally, I pull all of mine off my old vehicles and block off the port with a homemade plate and block off the vacuum supply. That way I don't have to worry about the thing being stuck in a partially open condition (which will cause the skipping whether the vacuum supply is connected or not).