Good post.

Alldata is the same as Helms FYI. Chilton's won't provide any extra help.

I think the fact you're overlooking is that you're spending hours and hours on this to save yourself an hour of easy labor. The intake manifold is a very quick job and just because your EGR valve entry ports were clean does not necessarily mean that the EGR ports in the cylinder head and manifold are clean. Taking off your intake manifold and cleaning it up should be routine mainttenance anyway for the paranoid car enthusiast.

'Insufficient EGR Valve Lift' indicated that the EGR valve isn't able to lift to the fully open position, either due to air blockage, mechanical or electrical failure. If you clean out the EGR ports you can completely eliminate the possibility that it isn't receiving enough exhaust gasses. It seems as if you've already ruled out the electrical possibility. That leaves either mechanical or a bad ECU. Your dealer will probably charge you a pretty penny to swap in a known good ECU and troubleshoot it, and EGR valves are pretty expensive. As any mechanic would say, do the cheapest fix first and work your way back from there. Clean the EGR ports in the head and manifold, then see if the problem persists.