Also, agree on how the property will be used, who can live there, and under what conditions.Contribution Reconciliation: Determine a process for handling situations where one party cannot meet their financial obligations or if there are significant discrepancies in contributions to expenses.Legal and Professional Fees: Decide how legal and other professional fees related to the purchase and management of the property will be shared.Taxes: How will the tax advantages be divided?

The off-the-market owner & his project manager realized a price discrepancy 1 day prior to closing and they informed the title company to not to complete the Master SS.How long can sueing a seller under specific performance take and what are some options ?

I think the other discrepancies are likely from these inputs:-closing costs at 5% would be too high for this type of home. 

County records and software listings typically provide the total square footage based on documented measurements, which in this case is 1,795 sq ft.The discrepancy arises because the seller claims the downstairs, used as a business space, is also 1,700 sq ft, making the entire property 3,500 sq ft.

What are the negative implications or downside of this discrepancy?

So they wrote a letter to the landlord insisting on a rent reduction of $100 based on what they called "rent discrepancy".

The same discrepancy may not be true in other markets.

As far as any discrepancies between the exact current value of Tim's portfolio, I can only say these numbers were taken as a snapshot of then current positions.

Any discrepancy over or under is dealt with the following year when the annual budget is adjusted. 

if you were worried about them trying to take money from you, then you should have been smart and put a meter on their water pump after you told them to flush it out or whatever so that you can gauge how much extra you cost them and then take that off the rent and then there's no discrepancies. it was completely due to your negligence that caused them an inconvenience and a health hazard. not sure we're all these other landlords get off assuming these are just cash grabbing freeloaders when they didn't do anything except do their part and move into a place and pay rent.so you can benefit from them doing so.