If you condense the question it seems to be a decision around total return vs. total risk. 

Contractor brought up the important point that just covering it up with cement board and trimming out remaining upper 2’ section means that condensation from cold weather outside that would naturally form on the inside of the covered up window section would just run down to the bottom ledge inside the covered up area, and even if the ledge is waterproofed, the water from condensation will just sit there for extended periods since there would be no airflow to dry it properly.

If the problem is severe enough, you'll see evidence of the problem with discoloration of your new flooring or even water ponding on the floor.Keep in mind that water can also condense on the basement walls adjacent to your new floor.

The condensed issue centers around decoupling of agent commissions, or no longer allowing seller's to pay the buyer's broker. 

In the case of the HVAC, I could replace the condenser this year (<$2500) and the air handler (also <$2500) next year.In the case of the roof I could replace the half of the roof that looks more deteriorated this year, and replace the rest next year (also <$2500 per year).

This means that I pay for the water, gas and electric to cool the condenser in the summer.

It's an item I see, and honestly MUST see, in our analysis spreadsheet that below is a condensed snipet from a recent one.

The AC condensation pipe got clogged and overflowed.

The key to Lockport is buying on the right street, its a very condensed city and a tenth of a mile can make a big difference in rent.  

i have a basement where i used cassette mini split which throws air in all 4 directions as its a long 20ftX40ft space. in the other adjacent room i placed a wall mounted split. both of them have one condenser unit outside with a heat pump. its easy to maintain but its double the cost of the typical HVAC unit. for me a typical 1.5 ton unit costs around 6k unit and duct and labor. but with the ceiling mounted 4 way and wall mounted one way Mitsubishi costed me around 12k.