2011 Mazdaspeed 3 Misfire (P0300) After Engine Swap

Hello! I have been searching for advice on how to fix this all over the internet, and to no avail. Any information or things to test is greatly appreciated. I recently had a shop do an engine swap into my speed3 and now I am getting some error codes and KR. I have included a data log for reference.
Year/Make/Model: 2011 Mazdaspeed 3
Mileage: 140,000 (55,000 on new engine)
Location: Somerset County, Pennsylvania
Concern: Misfire codes and high KR (spikes of up to 6 when pushing the engine but easy driving can keep it <2.)
DTC's: P0137 and P0300 (and a low coolant temp code, but I figure that due to a bad thermostat)
Modifications: Cobb intake and airbox, Autotech HPFP internals, 3.5" turboback exhaust (Corksport)
ECU/Tuning Software: Stock/accessport
Tuner: Stratified
Is the concern intermittent? No, every time it is driven.
Can you duplicate the concern? Yes, every time it is driven.
Recent Repairs: Engine replacement
Correction: 0.026" NGK Step 1 spark plugs

 

So that has the wrong data log file, check this one for the correct one!

 

What exactly is this log?

It appears you are at partial throttle during the whole thing. How are you coming to the conclusion that 6 KR is an issue and where are you seeing the 6 KR?

If you were seeing 6KR on a WOT log I'd agree that's something you need to address. Seeing 6 KR as a max value on the AP while just cruising around is not uncommon due to the way the ECU logic works on these cars.

https://www.stratifiedauto.com/blog/knock-retard-kr-explained/#:~:text=Essentially the KR value is,it may be something else.