You've started down the road and it certianly sounds like a phaser issue. I own an '04 f150, which I bought fully understanding this issue. My engine is noisier than I was previously used to and makes that diesel like sound when fully warmed up in confined spaces. Based on everything I've read and can get my hands on, I'm choosing to do nothing different. No $2000 repair bill that may or may not remove the dieselish sound. Regular oil changes every 4-5000 miles with name brand 5w20 oil and a motorcraft filter. Most cases of failure I've seen have occured when the engine was neglected (lack of oil changes, and debris builds up in the VCT system) or driven hard. My truck appears to fit neither of these scenarios.
Ford did ackowledge the issue and made a change to the phasers sometime in 2005. They continue to indicate it is a noise issue only.
Life is a lot easier once I figured out how to stop worrying so much...