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Hello, there are a few things that could be the cause, a tight valve/ low compression on one or more cylinders, a leaking headgasket, sticking EGR valve, leaking cold start injector.
Does it seem to run rough one one or two cylinders only, have you tried to isolate which cylinder may be the problem by shorting out each cylinder one at a time. If the idle just seems erratic with no particular pattern then it may be an egr valve problem, especially if it clears up after accelerating and then returning to idle normally, at this time I suspect that this may be the case. If the misfire can be isolated to a particular cylinder then it's not an egr problem but may be a loss of compression in that cylinder but in that case it would idle the same all the time after warm up, this may not show up on cold starts because of the fuel enrichment and fast idle associated with a cold engine.
Was this rough idle there before, was it the reason the parts in your original post were replaced or did this happen later. It sounds like there may be a small vacuum leak still, recheck all the hoses and if possible check the PCV hose on the valve cover on the passenger side. As a last resort I would recommend checking the valve clearances even though the compression may not show this, valve clearance will change when the engine warms up so a valve may have just enough clearance when cold but tighten up as the engine heats up and then not seal completely. Another possibility could be a cracked or broken valve spring which will also not show up on a compression test.