2011 Prius clacking and misfiring after engine replacement

Before I explain I want to reference there is a forum member by the name of cosmo tigato who may have experienced the same issue I’m thinking I’m having but I need other people to catch me on my thinking and see if I may be wrong. So the issue I’m having is as the title is explains a leak down test and new engine was all under 10 percent and I’m assuming I did the leak down correctly old engine was 25 percent and 30 on mid two cylinder so that was compression loss from HG I’m assuming. However I have checked everything you can think of on this Prius engine and nothing has been the issue I tried upstream O2 sensor swapping back to my OG fuel injectors swapping for brand new spark plugs swapping coils does nothing just unplugging them stops the clacking I’m at a loss here any suggestions or questions are welcome I’ll answer them all to get to the bottom of this

 

Follow-up note: when MG1 is spinning the motor, you can't hear any clacking, and when you put it in drive and floor with the brake held, the engine smooths out at 2500 to 2700, and I can't go any higher in RPMs. This feels like a combustion-related issue for sure, I just don't know what's causing it in just the middle cylinders. As I've stated before, the leak-down test passed on this new JDM engine, so it can't be compression causing it has to be fuel, air, or spark