How long have you owned the van, it sounds like you just got it and only filled it up once... maybe twice.
Anyway, my 1998 is having a similar problems as you. Ever since I bought a new engine. It actually is doing better, but every once and a while it has a bad day, where it stalls and stuff. The guy who put the engine in, said He can't figure it out. He tried a few things... coil pack, Crankshaft pos. sensor, throttle pos. sensor, and a few other things.
I'd have to tell you the chances of you needing a new manifold are very slim, unless you have a super/turbocharger in the van. I'd suggest replacing the IMRC gaskets, and inspect the fuel injector o-rings. You can do it yourself with a gasket remover/installer tool, gaskets, a torque wrench, and a few socket wrenches. I still gotta do my upper IMRC gaskets, because the guy that did my engine told me he replaced the lower gaskets, but not the upper gaskets. (He thought they were ok...but I think they may be bad). In my van, I'm wondering if the O2 sensors are bad, or the catalytic convertors are clogged.
I am also wondering it you got some bad gas in the tank, or maybe you and me have a related issue. Ford can definitely get you new manifolds, but they are pretty much $1500 (get a new-to-you windstar for that). If you really need manifolds (you most likely don't) go find a junkyard and buy them for ~$30. Try getting the gaskets changed out... unless you think it may be something else. Ask yourself: What parts may have been changed to cause the problem?
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1998 Ford Windstar GL 3.8L 253,100 miles
2005 Toyota Prius Package 6 1.5L 135,000 miles
2006 Toyota Sienna LE 3.3L 36,000 miles
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