an exhaust leak would make your fuel trims lean, like +16.
I don't worry about my stft's. even ltft's can be ignored sometimes, like when in deceleration enleanment.
I would often start a scan right after I reset my fuel trims because they would go to 0, and then when they relearned, the actual number would replace the 0.
also, I never set my PE to 100% because I wanted the data from wot runs, I just never went wot until I had everything with 5% of 0.
edit for additional info: You NEED to add Cylinder Airmass to your graph and/or to your channels so you can get accurate data on timing advance and knock retard.
I'm not sure if you need to be scanning for burst knock, I don't actually know if that was in the programming in 2004