My rep at the store will help me to lay out the space and even do a quick rendering for me. 

@Joshua Biondi I think my advice will be a little counter-intuitive but lay out for the realtor if there's anything that you don't know about navigating a real estate purchase. 

After speaking with the folks at the planning department they warned that my desired layout would be quite the undertaking.

We would love to hear thoughts from anyone and everyone, but obviously thoughts from those who have done something similar or have investing/rehab experience in this part of the country would be greatly appreciated.If we were to go forward with this plan, we would of course need a contractor, but we also think it might make sense to hire what we called a “rehab consultant” – someone we could hire on a fixed fee basis to help us choose specific countertop materials and designs, appliances, and bathroom rehab layout.

I'll take a lower cap rate because I want a newer build, to postpone capex expenses, to get a more modern layout, and generally ensure that I can have full occupancy.

Well forget the Electric heat, agree with @Max Tanenbaum on that, it will make it tougher for you to rent. you can look into as @Anthony Nguyen said, wall units that do both heat and a/c, depending on the size and layout of each unit. you can do forced air, one in the attic and one in the basement. or remove the old and install two smaller units and run hot water baseboard heat to each unit.

Your parcel is a triangle shape, which doesn't do you any favors for a parking lot layout.

It was converted to an open concept layout with a huge master suite and 4 bedrooms with 2.5 baths.I didn't have many contacts and had people trying take advantage of me so I went through two electricians, plumbers, and carpenters.

Bad layout that couldn't be easily fixed.

I like the layout and the details once you click on a property to view.