OUCH!!! Sorry to hear about the lens. Glad to hear you fished it out. Canon's reply doesn't sound optimistic. Are there independant repair shops in your area?
Glass lenses won't be affected by water. Some materials used industrially as coatings on glass can absorb water and will take up to a week to fully dry out. Can't say for sure whether any Canon coatings come under this heading or not as they are not exactly forthcoming with information as to their formulations. Any dirt left in the mechanisms will be the death of precise alignment and smooth operation. Looking through a copy of the parts manual for the lens some of the guides for the zoom and focus barrels are sorted into tolerance classes of 0.01 mm (0.0004"). Tried to upload it as an attachment so you could see what you're dealing with but the file size exceeds the limit. The title of the document is
EF 100-400mm 1:4.5-5.6L IS USMREF.NO.C21-9961

It is available online from some sites for no charge although some sites will try to make you pay for it. A Google search should find it for you if you wish to look it over.

Hope things work out for you with the lens.

Jeff