[wiswind]

Yes, that is the vaccum line to the EGR valve.

A slight miss can be real tough to track down.
A fuel pump issue can crop up under higher engine load......less intake vaccum, the fuel pressure regulator will call for more fuel pressure, so that is when a problem with the fuel pump may show up.

I am not familiar with the BG44....I have heard of it....but have not used it.
The Berryman's has solved a slight miss for me several times.....which is why I sound like a broken record about it.....a cheap and easy thing to do.
The windstar seems to be prone to dirt (tar-like) inside the "end cap" over the spray end of the fuel injectors.

The EGR ports (sounding less like your problem as the EGR valve test made no difference) on your 2001 will look the same as mine.....the upper and lower intake look different, but you will be able to identify the EGR ports very easily, once you get the upper intake manifold off.