So for instance one price for paint and dry wall, a price and steps to be completed to redo the bathroom.I would sub a ton of stuff out, get an electrician to bid electrical, plumber to do his thing, cabinets, counters , ac, roofing, painting, tile, flooring, framing and drywall etc.

I want to get the houses dry ASAP and then what to keep them from getting moldy?

Brush your teeth and floss everyday.The same goes for real estate.HVAC units,swimming pools,termites and critters,and appliances need regular inspection and maintenance before they fall apart or rot away.The roof should be inspected after every harsh winter to check for minor damage to repair before it eats away the entire roof over time.Looking for small problems to fix every 6 months can keep your property healthy longer and your cash flow swimming.

Yesterday they found mold and rot in the basement and the contractor on site said they'd likely be tearing out the entire rear wall (interior and exterior) as well as a lot of interior wall area of the unit to make the full repair.  

If you or the market hits a rough spot, and you are forced to sell at a loss (bring cash to the closing or short sale) or give the property back to the bank (foreclosure or DIL), you WERE "over leveraged" ... figuring that out before that happens is the trick :) And no, cash flow alone can't always prevent such an occurrence ... cash flow can dry up in an instant ... it can normally get restarted provided your initial projections were not that far off or too tight (which they are in the OP's case IMO), but how long and how much money it takes to get it flowing again is a tough thing to answer ahead of time.

It feels like flip ops are drying up.  

Is it purely local, such as convenience stores, laundromats, dry cleaners, or something wider, such as Supermarket, hardware store, paint store.2.

Sometimes I take them down but on 2 occasions I did a double close.. but I made sure I had the powder dry to close... lest they just let my contract die and swoop in and grab it..

As long as the floor is solid (no holes or rot) you should be able to install a wood laminate floor on top.

The biggest concern with a well is that it can run dry or go bad in which case you have to either drill the well deeper or drill a new well.