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Winnebago is equipped to provide OEM parts for almost everything they've ever made, at a price, and sold through a dealer. Chances are, an aftermarket E-series running board is going to be much less expensive than having Winnebago run off the OEM replacement part.
Lichtsinn Motors in Forest City, Iowa is a Winnebago dealer just a mile or so from the plant. I have purchased several parts from them. They may be able to help you.
KIT CARSON GOOD SAM LIFE MEMBER USAF VETERAN ARS: KE5VLE NORTHWEST LOUISIANA
A 2000 Minnie Winnie is most likely on a Ford E350 or E450 cutaway chassis. This chassis was also used with the more common Econoline Van. If it were me, the first place I would look for a running board would be a local auto recycle yard.