You are going to have to allocate the brokerage commissions between the owner-occupied units and the rental units.
The mortgage balance would be disregarded (not factored into the calculation) unless assumed by the purchaser of the relinquished property.
Obviously, you can use the home sale exclusion for the owner-occupied unit provided you have owned, and used the unit as your main home, for two or more years leading up to the exchange,
