UPDATE:
I Don't have the car back yet to confirm everything is back to normal, but since I've been living on this forum while trying to diagnose the issue, I feel I owe an update.
What was discovered is that part of the lower timing belt cover broke off and went through the Timing Belt. This cause the timing belt to skip a tooth. Based on further reading and investigation, many of the symptoms I've been dealing with could be explained by an out of time engine.