If the properties arer less than 5 units, they will comp other properties that are similar in size, bed/baths, and condition. 

One way would be to have 2 loans  that gives them the cash they need and reduces your debt payment in a 3 or 5 year note to cover that down payment they need  GIVES THEM THE CASH THEY NEED NOW AND A SHORTER PAY-OUT ON THAT 

The Basic Allowance for Housing (BAH) which is basically a stipend the military pays to service members to cover the cost of housing generally covers the rent and often times utilities and military folks are willing to use that to cover rent. 

Set exact same year range, size, beds, baths, area and see what is available on the free market? 

the only thing I was trying to avoid was any major costs to repair that wont be covered with there security deposit .

While to be Boston proper you are looking at some areas that are $1000/square feet you can find a lot of value in some metro areas such as Roslindale - 2 family with 5/6 beds can go for 5-600k in fair to good condition and that’s a nice middle ground location.

Any signs of previous problems being covered up, or band-aid repairs?

Current occupancy just covers operations so they are basically milking it as they can and waiting for the axe to drop.

To cover your costs of being an agent, you probably only have to close one deal per year.

I would imagine they've made you sign a waiver for such occurrences, but their E&O coverage should cover this.