Land in michigan is less than in texas , north texas.I will give you examples on cost differences.Material prices are the exact same price if not a little less.texas framing price per sqft $2.00plumbing $9500hvac $9500concrete Labor only $2.00 per sqft  Concrete $180yd 5 sackdrywall $10500Electric $8000Ok here are the michigan prices , better sit down.framing $13.00 sqftplumbing $25,000hvac  $20,000concrete is about the same for materialdrywall $20000electric $25000Both quotes were for a 3/2/2 home with 6/12 roof hipPeople in michigan wonder why houses are so expensive , its because of the sub contractors.The plumber only has about $5000 worth of material to do a whole house but yet there still asking for $25000

One other thought, how old is the roof on your rental?

It even has brand new windows, roof and HVACAsking price is $470k.

We opened it up, made a nice kitchen, changed the flow of a bathroom, new floors, paint, roof, and deck.

Should this issue be a partial responsibility for their absense while leaking and should we deduct some cost from them?

The roof, HVAC, plumbing and electrical are done. 

I would recommend you get way into the weeds on your due dilligence- septics, roofs, subfloors, hot water tanks, drainfields, etc. 

We both have some home repair skills, but would likely need to hire out larger work such as electrical, plumbing, roofing, siding, etc.Thanks for the help!

The water leak was causing the flooring to warp.

New roof, new siding, concrete patio, retaining wall, deck, windows....made it look nice.