Weird knocking

Is the motor oil clean and full? As far as a knock, a trained ear can usually identify it if is a bearing issue. As you are most likely aware, low oil pressure can cause it as well.

It's really hard for me to say without hearing it. However, if it wasn't related to the engine itself, it may have been something like the release bearing on the clutch. Did you drive it or note anything that changed the sound? And believe me, I would want to know, too.

Let me know.
Joe

No, It just stopped after it got warmed up enough, it shakes back and forth in first pretty bad, and in a higher gear is sounds like I’m tapping the gas pedal over and over when I’m just holding it to a constant rpm.

Based on everything you have mentioned, I'm questioning if there is a timing issue being caused by a sensor or actuator. If far enough out of time, you can get a knock and based on how it is running, that can also be attributed to it. Have you checked for diagnostic trouble codes? Is the check engine light staying on when the engine is running? Have you checked for engine vacuum leaks?

Let me know.
Joe