Stumped on knock noise

How many miles? How long have you owned the car?

 

Wow lots of miles.

How many times have you run the engine oil really low so low the check engine light came on?

Those are missfire codes multiple missfires that move around are sometimes blown main bearings causing lots of sub harmonic vibrations so the crank/cam sensors are unable to properly decode there positions which when the ecu see's not as expected positions between the 2 will throw a missfire code.

I think you have a blown motor. See lots of those here caused by oil starvation.

 

You can use car-part.com you can get motors for $100-300 all day long for the 2nd gen.

 

So, you have these noises when idling or sitting at a stop light/stop sign, but not when driving at speed? Is the check engine light flashing during these times or is it solid?

 

As far as I'm aware, the only thing that causes a flashing check engine light is serious misfire. The only time I've experience this was when one of my plugs had an excessive gap due to losing the small iridium/platinum disc on the ground electrode, and it wore away.

Obviously you have a significant issue going on.

I know you replaced all the ignition components. Did you have all the same codes prior to the work? What plugs did you use?

Any check on fuel pressure?

 

If the check engine light is flashing when >35 mph, the system is still detecting "misfires". Real or not, is hard to say. One thing I've learned is that nothing is impossible. It could even be a timing issue, like worn guides, tensioner, a bad VVT or clogged VVT filter, throttle body issue, a vacuum leak? Just throwing ideas out there.

I think with the work you've done already, I would spend a bit of time making sure the fuel system is doing it's job. If that's good, I'd be looking for a big Vac leak.

Do you have Tech Stream so you could connect and look at the engine while it's running? Could also have freeze frame data available.

 

I've had to gen 2s with 280K + miles. Neither had any bearing issues, and both were treated much worse than how you report yours was treated.

A random misfire, like you're experiencing is much more commonly caused by weak fuel pressure, a problem in the fuel system or a vacuum leak, even potentially a crappy cat.

How does the engine run when you're driving?