Prius (2010-12) :: Knocking (Raptor Sound) At Intermittent Times While Driving

2010 Prius making knocking sounds. Not exactly the "death rattle" that sometimes happens when you first start the car.

* While driving, the sound reminds me of the Raptors in Jurassic World.

See example videos:

Knocking at idle (Knocking Noise starts at ~19 seconds into the video):
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Knocking while driving: (Good examples at ~24 seconds into the video):
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Knocking while driving with Torque OBD2 Monitors: (Noticeable example starts at ~28 seconds into the video):
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The car has over 300K miles and the problem started a few months back. At first the sound only occurred while driving under certain load conditions.

The problem would occur at intermittent times. Normally at low speeds with heavy loads (going up hill with low to medium acceleration). Also occurring for a short time when letting off the accelerator. Never occurring at moderate to heavy acceleration. Never at idle. Recently the shaking / raptor noise started to occur while idling.

* This problem is now easily created at idle each and every time the HV battery drops below 2 bars and requires charging. The engine change is immediate and starts and stops in sync with the extra load of the HV battery charge cycle.

Placing the car in the maintenance mode, the car will start and idle normally then immediately start and stop the knocking when it switches from HV charging to non-charging mode. There are no Check Engine light. Things I've done to troubleshoot the problem:

* Swapped the following parts with another working 2010 Prius.
** Coils and spark plugs
** VVT solenoid
** Cam Sensor
** EGR Valve Control
** Fuel Injectors
** MAF Sensor
** MAP Sensor
** Evap Control Valve

* Cleaned the intake manifold (It was full of carbon)

(This was done about a month before this problem started to intermittently appear).​ Prior to cleaning the intake manifold the car was shaking and misfiring under certain high torque condition and generating a P0304 check engine code). Once I cleaned the intake manifold the problem was fixed. I had no more check engine incidences and the shake was gone.