We initially signed a contract for asking price on the property and I subsequently asked for $20k break on the price based on the inspection results, which I thought was a fair ask and the seller signed the addendum accordingly.Now the seller is asking me for another $6k to cover costs of heating unit replacements (after further inspections done by the seller as required by the city) since the units are over 50 years old and cannot be brought up to city inspection requirements.

Not fair at all, but MA wants all rentals lead safe and they're doing everything they can to get them that way.With all that being said, check your state laws, not the EPA site.

I am hoping that by being part of this market (the military life) it will enable me to make smarter investments that will ultimately allow me to provide servicemen with better and fair housing.

We, as RE professionals can limit exposure for ourselves and our clients by implementing prudent due diligence on tenants; by ensuring our tenants are properly licensed, operating within the law and keeping their operations to code the changes of the DEA / DOJ seizing assets is (in my opinion) next to zero.

If you don't have a bank that has a branch in the area of the property, have them mail it in (get a money order), but ensure they know that the post mark date is not the date used for determining late payments, it is the date that the rent is in your hand that is the date used for payment of rent.

Agents don't want to get buyers who give them the run around, so they use this document as a way to ensure they aren't wasting time. 

Ensure to double-check what you expect the After Repair Value to be, so you can know, or have a good idea going into the deal, if you will get all of your cash back, or what amount you can expect to get back. 

They ensure that every point of contact on their service chain and their associates--lender, title, notary, remodel-- is extremely professional and painless as possible. 

How do I go about ensuring that at the time of closing, the total cost of fixing plus my fee for the fixing and coordination gets into escrow and I get pay out at the time of close and my brother only gets the remainder from this sale?

If those are the requirements you have for ensuring that a deal will cash flow, and possibly cash flow better than your conservative projections, then stay true to them.