I'm not sure I understand what you're saying about vacuum at the yellow hose. That hose gets its vacuum from the 'controlled' or switched side of the controller. The controller electrically opens/closes vacuum to that hose which then supplies vacuum to the EGR valve. With that line unplugged from the controller, there would not be any vacuum from the EGR valve end of the now unplugged hose as the controller is the source.
I think the term "occilating vacuum" is something you'ld only see with a guage, you'ld see the needle fluctuating, not steadily at one spot. I'd then suspect that'd be because the controller probably opens/closes vacuum very fast vs just opening and staying opened. I have heard those things make clicking noises before so that's probably OK.
I've never noticed where an engine idles rough after clearing codes, shouldn't really effect idle so that in itself makes me wonder if there's possibly something else going on here or if perhaps your EGR valve might then be sticking afterall. Did you try directly adding a (known good) vacuum source to your EGR valve, like run a piece of hose from direct engine vacuum to the EGR valve with the engine idling? It should noticeably idle rougher with the EGR valve opening and smooth out again when the vacuum source is removed from it. A reason why you'ld want to use a vacuum tester for that vs the method above is so that you can also see if the valves diaphram is holding vacuum. You can't know that otherwise.
If your EGR valve was sticking, staying opened, that would cause rough idle and lack of power as well.
Being that you don't have a vacuum guage to see if the controller seems to be occilating vacuum as it should, all you can now do is test the EGR valve as I mentioned above to see if it's opening/closing correctly. I'd say that if it is and that it doesn't seem to be sticking at all, I'd then suspect that your controller is malfuncting. Both the controller and valve cost about the same, I was quoted $170 each so I'd hate to be the one guessing wrong from here as I don't want you to waste money. I'd suggest buying an inexpensive vacuum guage or tester from an auto parts store as it should help check that controller if your EGR valve seems OK now.
Hope this helps?