After I get my rent and W2 income and subtract out the expenses on average I save about 1500 per month.

Do I subtract all improvements(costs) from the sale price.

If you subtract my $50 deductible, which I had paid, and the cost to purchase the replacement, which shipped directly to my house for only $180, I made money on the deal. 

It subtracts the beginning value from the final value Say you paid $500k for a property and sold it for $1M.  

Then you subtract the $280,000 I owed at that time which left a HELOC amount of $78,000 ($358,000 - $280,000 owed =$78,000).  

In my experience staying hands off is fairly typical, I expect that you plan to have more than just one rental so the cost of being hands on would keep increasing and subtracts from your bottom line. 

To get your cash on cash return subtract the principal and interest payments from the NOI.

Is there anything wrong with taking the 100% bonus depreciation on these (and subtracting their value from the total purchase price to calculate the building basis)?

My thought was:1 - I put the down payment and assume the mortgage.2 - Contractor (no skin in the game at this point) buys materials to complete the necessary upgrades3 - When it is done we sell the property and subtract the down payment, material cost, mortgage payments, utilities, settlement costs - and then whatever is left we split.  

By subtracting the ACV from the RC you get the amount of depreciation.