I am having the exact same problem ever since I replaced my turbo as well. Only im running a k04 on a stock ecu

I haven't gotten the misfire code till yesterday, and its been doing it since last week, but do you have a boost gauge installed? Im very positive it only happens when you boost over 10lbs, or at least thats when it does it for me.

I would suggest a diverter valve change/upgrade. I ordered mine last week and it should be here in the next day or two. What I think is that your stock tuning has the boost at a low level, but since your dv is already broken you feel it with slightly with stock tuning, and even more so with a chip, because it ups the boost.

Someone else have any input? Feel free to correct me if im wrong.