Keep checking for a persistent misfire in the fault codes. Injector 3 went on mine. Naturally no amount of plugs and coils thrown at it solved the problem!
I caught mine early though and was just a hiccup going into boost, not a full on stutter like yours does/did. I replaced all 4 as I'm not going in there again!
It misfired at idle (intermittently) too, but it was a proper and continuous misfire, not a general lumpiness that these engines can sometimes have.
When it started misfiring at 2,500rpm, could you drive through it? Or did pushing the pedal more not increase acceleration, or slow it down? Just asking as I've seen that happen from a blocked cat before. Can't remember what exhaust you've got on yours!
I could drive through the stutter on mine, so the injector was kind of working better with a higher duty cycle. Just had a dead zone.
Keep digging, I'm sure the cause is there somewhere!