Such as remodeling a bathroom, you can pull a permit for it but if your just doing a cosmetic remodel (tiling, new vanity, mirror, bathtub etc.) it would have likely not been an issue unless you are changing the layout and moving around plumbing etc..

The interior layouts are pretty much all the same.I'm not quite done with inspections yet, so I don't know the condition of the electrical and mechanicals, but I do know the that the interiors all need updating (floors, cabinets, counters, sinks, paint, etc.)The problem is is that I'm out of state.

We are putting roughly $40k into each unit which includes new floors, kitchens, updating bathrooms and moving a few walls to open the units up into a more modern layout.

A better kitchen layout would have brought much more money.

The formulas don't work since converting it to Excel, buy it's pretty intuitive.

I have gotten several bids on installation but I just kills me to pay for something I'm 70% sure I could do. is it posable to hire a contractor just for advice on layout and as problems arise?

A lot of height/independence height townhomes/houses are this way and there you will find national builder to customer low volume builder to smaller builder building houses on pier and beam .Also (to me) there isnt anything call high end builder ..instead high end design ... cause all houses will be built by same set of folks BUT the differentiating factor will be in deign and/or layout ... pay close attention to that one and sit closely during civil/architecture drawings. 

I am convinced you wont find anything as robust yet as intuitive to use.

For sure it sounds as if the garage was converted into bedrooms without the city/county department approving the changes, I  would do some research at your local building department and pull up any information, usually on microfilm,  regarding the duplex construction building layout, and compare the existing building layout to what you find.  

Is there software that I can simply feed the size of the units I am looking to build inside the 8000 sq ft footprint and the software can determine best layout (accounting for elevator etc?)