2012 Prius - Cylinder 4 Clunk

Kind of a long story, but I recently did the head gasket in my 2012 prius. The headgasket showed signs of being compromised for cylinder #3 where coolant was getting in. The head gasket visually showed signed it was compromised at cylinder #3. Everything is reassembled, but it makes a weird clunk sound. Unplugging different coils led to the issue being isolated to cylinder 4. The engine runs fine if the coil for cylinder 4 is unplugged. Prior to the repair, cylinder #4 did not have any issues.

Below is a list of stuff I've tried so far -
- compression test, all cylinders are 170psi +
- swapping coils, sparkplugs, injectors with other cylinders to #4.
- reset the computer by unplugging the battery
- checked the timing. The timing marks line up for the two cams and cylinder 1 is in in the upmost position by putting a stick down the cylinder to measure
- Put a camera down all cylinders and the intake valve section, they seem normal
- Turned the crankshaft by hand and it rotates fine without abnormal sounds
- When the engine cranks when the electric motor runs, there are no sounds, appears to be normal.

There are a number of CEL codes -
P0031 - Heated o2 sensor
P0102 - maf sensor
P011 - intake air sensor
P0351, P0352, P0353, P0354 - coils were unplugged/removed for the compression test
P0403 - EGR

The CEL codes appear to be from unplugging and re-plugging various sensors/devices. Pressing the gas pedal while in park does not rev the engine.

Any thoughts?