Then last week we get that big wind storm , and I lose lots of shingles off my personal house and the house with the new well .  

There is another house in the community that replaced their roof with composite shingle but the HOA made them take it down.

You easily could have had wind blow off shingles and it cost $500 to repair, you wouldn't charge the tenant.

New shingle roof - $6-8 per sq ft New high efficiency furnace and all new duct work with 8 reagiters - $5000-7000New high efficiency tankless water heater with new 1" gas line. $3500-5000New hardwood flooring with stain - $10 per sq ft. 

Shingle, barrell tile, metal, etc?

Dumb stuff I've done: ages ago when I bought my very first house, it needed exterior paint and shingle molding replaced.

The problem was that it was a Victorian home from the late 1800's, and during the 60's, a prior owner installed cement shingles that were loaded with Asbestos. 

The RE broker found someone reputable and got back to me with a quote of $45K for the big office building and 40K for the smaller office building (would need to be done in next 3 years) – this would include tear down, using shingles that last 30 years, repairing mortar joints on chimney, etc.

These included under sinks, inside electrical boxes, plumbing joints, insulation, roof shingles, broken window seals, the whole nine yards.IF, you trust they’re doing a thourough job and charging $100 or less, MAYBE I would keep using them.

There are metal shingles and standing seem roofs.