Our plan was to turn it into a rec room and not count the square footage.

They are a combination of roof pitch, dormer count and sizes , covered porch square footage, attached garage, 16 inch eaves, 2x6 construction, driveway with sidewalk leading to front door and more.

You should pick comps based on the numbers (sq footage, beds, baths, #fireplaces, deck, #garage stalls)Stay within +/- 800 sf. and then adjust for $25 per sq ft difference for any above ground sf.  

I would see what houses with similar square footage taxes are.

You'll also need to hire someone to create as-built drawings for your house (so you can show square footage, locations of smoke alarms, fireplaces, how many beds, etc. and same for your property to show setbacks, easements, parking, locations of trash cans, etc., which you will need to submit to the county with your application.

We are looking to build a flex space and would like advice on the ideal sq. footage. 

What you are describing doesn't sound too extensive and if you are not looking to expand the footprint or add square footage it should be pretty straightforward and more or less cosmetic (new siding should perform better but still straightforward). 

Banks have been offering us 390 based on our number or rooms and square footage, which in the new neighborhoods are selling easily for $410-450.Buyers in the area are wanting houses with a garage, ours doesn't have one, they want more of an open floor plan, ours is a floorplan from the 1950s which is more compartmentalized. 

The city is fairly helpful when dealing directly with home owners but unless you are adding square footage (pop top/back), I don't believe you have to adhere to green points.

One crucial piece of information the Planning Dept provided me with is that if the buildings are located anywhere within the property lot's "setbacks" (specific square footage adjacent to the property line), the city would not allow the buildings to be permitted, and could even order them to be tore down.