My opinion only, and it is worth what you are paying for it.
1. It is an arms-length transaction. Based on what you explained, there is no real tie other than the buyer and seller knowing each other, so how is that any different than purchasing a property from an acquaintance? The lack of marketing is a separate matter, and you should include something in your comments about the lack of market exposure, so the contract price has not been market tested.
2. This sounds more like a hobby farm. As per your comments, the client has not provided you with any historical income or expense statements, nor have they given you any income and expense projections for a commercial stable. Typically, hobby farm owners take advantage of certain tax deductions that can offset the cost of their investment in the particular hobby. The income generated and the deductible expenses can be an incentive for some buyers if they have a use for the particular improvements. I would strongly recommend talking with your client, discussing your research and the results of your appraisal, and ask them how they are viewing this purchase. Is the client considering the potential income and expenses of the operation in their loan decision? If so, ask them to provide you with all the financial information and then try and find a CG that will work with you on completing the report.
Your value may be coming in low due to your giving inadequate value to the specialized improvements. If you haven't, you may have to value everything other than the specialized improvements using the sales approach and then rely on the depreciated cost approach to value the specialized improvements.