Well, I took another look at the Contour. I discovered that when she starts the car, the vacuum secondaries don't change. It appears that either the vacuum servo has a hole in the diaphragm or there is no vacuum to it. When I had the intake off, I did operate the linkage to make sure the plates were clean, so I know it's not seized. I didn't however hook a vacuum pump to it and see if it would operate and hold vacuum.
With the car idling I removed the vacuum line from the EGR valve and pulled a vacuum on it. It held vacuum, but had absolutely no effect on the idle of the car. The engine was up to temp though, but I believe the EGR should still be closed at idle, even on a warm engine.
So, I figure I'll be pulling the intake again and chasing vacuum for the secondaries, at which time I'll pull the coil packs and try to find a home for the melted vacuum hose.
-Rod