The value of a well is usually factored in under the "site value" in the cost approach section of an appraisal. Sometimes each improvement is specified a (well, septic, land value, etc), but sometimes not. If that is already factored in, then the seller needs to just realize they have a higher opinion of their property than the lender will, and decide whether they really want to sell it. Personal property that's included in the sale is usually noted on the offer, but in this case, you might want to separate the water shares (not sure what that means) from the real estate contract, which should bring sale price closer to appraised value and buyers may be able to get financed. let us know how you work it out...
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REO Broker since 2004
"And think not you can guide the course of Love, for Love, if it finds you worthy, will guide your course" K.Gibran