Major BS on your dealer. If you bring your vehicle in, it has the clunk, you fall under the parameters of the tsb, then there's no reason why the part shouldn't be ordered or installed if they have it. Never have I ever had to call an engineer and have him agree that that's what should happen. The only time an engineer is called is when a tech calls "hotline" for an issue that's got him pretty much stumped or to see if there's anything related that's not already a known condition. Take it somewhere else if they want to make you jump through hoops.
There's another dealer fairly close to the office. I can drop by there during lunch to see if may be they can help me out. I agree, the original dealer is being a pain in the butt. I thought surely after going up the chain a bit I might get a little help and may be coordinate the fix with my next oil change but, no...It almost sounds like they don't like doing maintenance or warranty work for people with ESP contracts.