(2/1 unit has a hot water heater in the basement, replaced in July 2017. 

Being new to this, I was really naive and thought, ok, we can replace the windows, remodel the kitchen and bathroom, and resurface the hard wood floors.

It turns out her old landlady in a similar situation had brought out a contractor and made a lot of noise about replacing the whole vinyl window, and finally charged her $70.00 for an entire new screen frame shipped from the window manufacturer.Same landlady who ate my tenant's security deposit and had never heard of giving notice before banging on the door.

Most of the other “financial engineering” is bunk.

I have a reliable and reasonably priced HVAC technician you can call for inspection, repairs and replacement depending on the part of Maryland your property is in.

We fixed the major things (mold, replaced carpets and flooring, painted everything, fixed the sunroom etc.)

Most likely replace the flooring, install some granite countertops, landscaping, probably knock down a wall.

Single family rental property was bought a few years ago for $42,000.In 2018, furnace and air conditioner were replaced at the same time.

Looks like it needs flooring, paint, countertops, cabinet refinishing (or replacement), roof repair, dry rot repair, maybe foundation repair, lots of wall repair, and possibly plumbing/electrical repair (nothing can be seen in the photos but common in that area).I agree with @Dylan Vargas that there is no money to be made in flipping this property based on your numbers. 

I used a mixture of new construction type or replacement type in both single and double hung depending on the application of the window.