Dang Eric, that some serious advice. Nice touch including the valve clearances.
The dealer has really been great to work with on the other issues so I feel like a heel for bringing it up but I don't want to ignore it and have huge $$$$$ problems later.
My wife is the one who will have to deal with getting the car to the dealer as it's less than 10 miles from her office.
I've already decided that it'll go back and I'll get their opinion on the issue.