I'm researching some Baltimore properties that have been rehabbed and permits pulled.

I have paid off $2 million loan in mortgages while there has been appreciation of properties as well I donot want to lose sleep when a few tenants leave or I have waterproofing or permit expense of commercial property of $30000 all of a sudden. 

No permitting (other than septic) or inspections.

Go to city building & assessor offices to see what you can dig up about the property, including past permits and inspections, tickets, etc.Make sure you get all tenant contact info and application info at closing.

Did he handle getting all permits, plans drawn, etc.?

When all factors  are considered in totality, the applicant's 2.7 income factor may be a "safe" risk, but if the other factors indicate a problem with this applicant's qualifications, he may prove to be riskier than you should permit.

Quote from @Robert Ellis: new builds set the price premium in every zip code I've ever studied. in addition new builds don't take 9 months. we just built a house in 60 days. we wait till permits are approved and shovel ready, investors buy land cash, entitle, contracts, negotiate with financing, place financing when we are ready and break ground. but we build the same over and over and don't go outside our Floorplans 60 days from Dig date maybe.

As @Bill Brandt mentions it's probably a bad idea to permit Great Danes in a 500 foot walkup apartment, so adjust as appropriate.

What is the practical process for getting permits for rehab properties?

These are usually legal for an owner to live in (as long as the bathroom is permitted).