It doesn't sound like you have an IID Tool. Maybe you should get one to read the codes on your own. It's a big initial investment ($500), but it'll save you time and money from driving it around and allowing you to diagnose it yourself.
If you have one, I'd clear the learned adaptation values. You made a lot of changes where you want to force reset the adaptation values back to factory and allow it to dynamically adjust to your driving style.
This truck is VERY sensitive to vacuum leaks. Leaks will cause it to do weird things, like engine noise, loss of power, random misfires. With the engine running just spray soapy water all around the PCV, valve covers, hoses, and hose connectors on both sides to find any leaks.
I ordered one today! You're absolutely right. I DO need one.