Well I think I found the real problem. I had the carpet out doing sound deadening, and did some test fitting of the engine cover to see where it wasn't seating right. It turns out the FLOOR was bent down near the driver's side engine cover toggle clamp. It is just a piece of sheet metal that doesn't have any frame under it.
The fix was easy - I just bent it up by prying with a 2x4, using the transmission as a fulcrum. This made the sheet metal "oilcan" a little but I fixed that with some scientifically applied blows from a mallet. Now the engine cover gasket seats uniformly around, and the noise is about gone!
As I have torn apart the interior doing sound deadening, it is frightening how poor the quality of assembly is on this van, mainly in how the trim pieces are attached. I may end up using some black sheet metal screws to replace some of the plastic push-pins to make things more secure, especially on the stepwells.
2009 E250 RB 5.4L "SilVan"