I don't know how much help this will be, considering I've never found a solution, but ..
When I first installed my FMIC and BOV without relocating my MAF, I had the worst idle/stalling issues EVER. Then when I relocated the MAF, hooray, no more stalling! But that was two years and many mods ago.
Recently, as the weather has been warming up, I've noticed the same thing as you -- my idle will SOMETIMES spaztically dip between 500 and 1000 RPMs. I haven't the slightest idea what's causing it. I have no vacuum leaks (I've checked a bajillion times like you), and even more puzzling -- I throw no engine codes.
Now, here's something that might interest you. I USED to throw engine codes .. BEFORE I replaced my wastegate actuator. Since then, I still get the spazzy idle on occassion .. but I do NOT get the engine codes anymore.
Granted, I'm sure the rest of my mods are different than yours, so our situation might not be totally related .. but still, it's something to consider.
One question -- when you throw your CELs, are you driving your car aggressively? That's the only time that mine would throw codes -- when I was really getting on the car.
EDIT: I forgot to mention that I have the hopes that my Unichip will help with this issue. I have little doubt in my mind that the bad stock tune only contributes to ALL problems us MSPers come across.