Then subtract cost of sales, 6% for real estate agent, 1% to 2% for closing costs, any transfer fees. 

If you really want to protect yourself you can contact REI Guard for a Builders Risk policy and just subtract this amount from the bottom line.

Cash invested: $98,600 subtract $2,300 I recieved from auction and $1,200 from 2 trips to the junk yard. 

If it's an investment property, major improvements will get added to your basis, so no immediate deduction, but will get subtracted out upon sale which lowers your capital gain eventually upon sale (or increases your loss). 

As a side note, 5% down on a $400k loan would make P&I closer to $2040 rather than $1900, and that doesn't include PMI or taxes.So say you rent out three of the units for $1300 = $3900 monthly income.Now, subtract 50% for expenses and you're left with $1950 as your NOI.Take out your mortgage payments of $2040 = -$90 monthly cash flowSo you'll have negative cash flow based on this very loose evaluation, and assuming you live in one unit.

These are percentage off of your rent so take that 400 and subtract 120 for management, 95 for vacancy, and another 120 for capital expense and maintenence.

Take the gross monthly cash flow of the property you're looking at and subtract 25%, that gives you the cash flow if you lived in one of the four units.

Taxes, insurance and utilities paid would be subtracted from the 700-800 gross.

Or where would these expenses be subtracted from?

Start with the comps, and subtract all the other fees and expenses...and profits.