As others pointed out, the timing was off one tooth. Redid the timing and resealed the timing chain cover. No leaks, no codes. Only thing I don't like (and it did this before) is when the engine is shut off by the computer (while still in READY, not when shutting off with the button) it makes this "shotgun racking" type noise.
Did it do this before I've got one that shuts off hard like that Not all the time either It seems to be when the battery HV battery is really low for whatever reason
If it's intermittent it's the nature of the atkinson engine. If it always happens, it's probably something else that you need to be concerned about.
It's almost like when the ECU shuts the motor off, it has to stop at a certain point in it's rotation, and when this occurs, it's not stopping where it needs to be, so the electric motor is slightly rotating it to this spot. Also, the Driver's side CV axle is in need of replacement, it's very sloppy. I'm not sure if any torque is transmitted to the axles when this occurs, but if it is, that COULD explain the noise as well.
Also had to order a new drain cock and seal for the top of the aftermarket radiator. I thought the new radiator hose and clamp I installed was leaking, the bleed valve hole is literally right above the house outlet.
Yeah, that could be the source... There's a "thunk" that I've heard many of older Prius have that when engine shuts off that sounds like the transmission dampener and axle.