It's hard to be positive with out being there but with what you are describing i would yank the engine and find out what is going on.
I have been called a overreactionist ( not sure if thats a word or not) but i have never pulled and engine that had a problem like you are describing and thought ... "man why did i do that"... I would be sure you are going to find something wrong...... I always looked at it like this. I would rather take the time and investigate then let it go on a wing and a prayer hoping for the best,,, and then destroying my good parts......
Is this a roller cam motor???
Is the by pass plugged in the filter adapter???
Can you post a picture of what you found in the filter??