I see visible rot on some of the exterior.

The kitchen sink had been leaking for so long that the entire kitchen floor was rotted out and I could see into the basement.

I subbed out the roof my self and when they took off the shingles the plywood was rotted so I bought all new plywood and new shingles on main roof and rear porch.

Any suggestions on how I should handle the situation if I do have damaged dry wall or doors?

We are now one week into the rehab as I type this.Current BRRR Numbers:Pre-closing Costs: $2,740Plumbing inspection (because the house needed to be dewinterized, $150)Home inspection ($525)Appraisal ($655)Electrical inspection (because power was off on the day of the appraisal, $150)CO and Smoke Alarm ($366.57)CO and Smoke inspection ($52.50)Rehab consultant ($840)Kitchen Appliances: $2,000 (estimated)Plumbing: $7,300 (estimated)Oil tank ($1,800)Water heater ($1,000)Chimney liner ($2,000)Re-piping as needed ($2,500)General Contractor: $32,000Roof replacementDrywall patching and painting of entire house (trim, wall, ceilings)2nd floor bathroom spruce-upClosing exterior door in master bedroom and finish sidingBuilding two closets in two bedroomsBroken window repairsWindow frame repairsScrape and paint area over bulkheadFinish floorsRemove and dispose drywall from basement spacesRear deck repairFront steps repairInstall handrail to basementFoundation masonry repair and paintingRepair cement stepPatch area of exterior trim near kitchenPatch two rotted window sillsCap extra basement doorFill in dining room windowAsbestos: $1,500Electrical: $2,000 (estimated)Closing Costs: $3,733Home Purchase Price: $149,000Total All In: $200,472Expected ARV = $250,000 (initial appraisal for rehab loan came in at $235,000)Amount I have invested in the deal = $50,000Expected Cash Out at 80% = $50,000The situation is still very fluid, as we still have at least three more weeks of the rehab in front of us, but the numbers thus far are still looking promising, despite all of the surprises.

There were some staining to the dry wall.

Banks let them rot, kids got in, a couple were stripped of electrical/Cu piping & yet some were left complete with all the tools, drywall & new HW tanks.

I needed to caulk, trim paint and the biggest thing was pressure washing the rear deck because the previous tenant had potted plants on it for 4 years... a bit of a pain because it's a very humid environment down here so wood rot is prevalent.     

Or it could be just a temporary freeze-related issue with the line between the well head and the house not being buried deep enough and freezing or it could be a separate issue: like Jaron said pump issues are more common than wells actually running dry.

But that dries up quick.