After the inspector walked it with me he said it is not major, just take care of it right away.  

I am looking for a reputable licensed home inspector available in the City of Baltimore.

Get on those buyer listsIf you get a good realtor, partner w/ the realtor to evaluate the off market deals along w/ the deals from the MLSLeverage the realtor/wholesalers network of inspectors, GCs, handymen..... to build your own network If you find a good deal consider partnering w/ someone w/ good credit on the deal.  

I am a licesened Home Inspector living in Bradenton.

They will likely send an inspector to show compliance with city code depending on the type of store fronts (e.g. a restaurant setup will have different requirements in many cases than an art studio, for example).I would certainly invest in getting individually city metered utilities so that the tenants pay their own utility bills and there is not some messy shared arrangement that you have to deal with.  

I was literally handing a check to the inspector when I received the call from the loan officer with the bad news.  

Why not just adjust your purchase price downward to reflect the inspector's estimated cost of the repairs in the inspection report?  

We did the inspection, paid for the inspection(  because the seller asked tenants to give access to the inspector, first time one tenant fail to do so, the inspector have to go to that unit on the second trip, cause us $150 more for the inspection), and requested the seller provide lease, which should have information for the deposit tenant paid, the rent, etc.

Any recommendations for a Port A contractor (variety of structural work) and/or home inspector?

I would use a reliable 3rd party property inspector for this which will cost you about $200 - $400 based on the size property.Before doing that, definitely have a local realtor that's representing you look into it.