Welcome to my world... So I have something similar but thought it was my Uni tune. I switched fuels, flushed through two fill ups at sonoco going for minimal ethanol; was using shell pretty much exclusively.
I ended up disconnecting my JB4 and stopped getting limp mode, however at about the same place I was getting limp mode my car sorta bucks but doesn't throw a light. When scanning the light was overboost which prompted the "WTF" in my mind.
I have RS7 Plugs and RS3 coil packs that I'll be installing in the next week or so. Past that it is on to the clutch to verify that it isn't slippage, causing some type of weird overboost; but that doesn't even seem plausible.
So ultimately I think I'm working with a very similar issue to you but I was stacking. No stacking, no light, but weird issue that feels like a misfire in the same range.
I'll keep you posted