Gen 3 2010 Prius Rough, loud idle, knocking

My son has a 2010 Gen 3. Started horribly knocking, shaking a few weeks ago. 225,000 miles. Was showing Generic Missfire codes and missfire on cylinder 1, 3, 4. Check engine light on.

Took to local shop. They recommended plugs, coils, EGR cooler and valve. $2600.

We took the car home and have done the following:

Cleaned EGR cooler.
Cleaned EGR pipe.
Replaced EGR valve.
Replaced Plugs.
Replaced Coils.
Replaced PCV valve.
New MAF sensor.
Removed and cleaned intake manifold.
Cleaned throttle body.
No codes showing as of now.
Check Engine light will flash when accelerating quickly.


The engine runs smooth at idle, but hiccups occasionally - feels like it missfires at around 18-23 MPH and 40 - 43 MPH.

What's next to explore? I'm ready to give up.

 

Forgot to mention that. I did replace injectors.
Visually inspected lines, and tried to put pump smoke through, but could not see anything.

 

Bought the car at 200,000 miles. Not sure if EGR had ever been serviced/cleaned before.
No done a leak down test. That checks the pressure under the spark plug to check pressure in cylinder?

 

We didn't really notice if it was low until yesterday. It was a little low, but no visible signs of recent leak. Have topped off and ran it for a little while yesterday trying to see if losing any coolant now.

 

10-4. Will explore looking for testing equipment. In the mean-time...

Next question:
I had said earlier that no codes were present. My son drove for a few miles this morning. Check Engine light came on.
PO304 - Cylinder 4 Misfire - Does any of the recorded data from when the code was triggered tell us anything useful? For example, 1006 RPM. There are other data points - using RPM as example.