If the P&L is not audited (or at least certified) then I would ask for tax returns and bank statements to verify them.Get financial vacancy numbers vs physical vacancy.

In terms of overheads, you should allow 5% of gross rents for vacancies, 5% for maintenance, $1550 for property taxes and $1000 if you want decent liability and wind/fire/theft insurance.Work backwards from there and you´ll have your bid price. 

Which account do you keep money set aside for cap ex, vacancies, expenses, etc.?

If you mortgaged the property, you should include a vacancy percentage in your numbers therefore covering any unknown vacancies in the future so you wouldn't need to worry about that. 

Other things that can effect value ..... what type of utilities, any capital repairs needed, size, market, upside , vacancy.

Vacancy fees are not common in the Atlanta market but there is certainly an argument to be made in favor of them.

If you were to examine the Business' tax returns or the Schedule E for 2 years, you will see if the tenants are having problems or verify that everything is great and that you can make a sound and solid offer.You can also discover if there were any deferred maintenance, legal problems, etc.Also, not every Broker/Agent will be on top of their game.I usually throw out the numbers given to me and just do my own, adjusting for vacancies, late payments/evictions, etc.Also, the Agent's fiduciary responsibility is to get the best deal for the Seller, not the buyer.

Now sure, if no capex happens and there is low-no vacancy, great  but you can't count on that.  

Literally no vacancy other than rehab time. 

Ultimately I am interested in quickly filling a vacancy for the highest possible rent, not getting the highest possible rent despite a vacancy.