I would do a dormer windows over a skylights.  

I spent 30 hours touching up small gouges in the walls, washing the tile floors, repairing leaky faucet, cleaning residue left on walls, light switches, and cupboards, removing trash left behind, cleaning vents, fan blades, replacing light bulbs, repairing blinds, cleaning stains from carpet, fixing broken drawer, washing garage floor, & cleaning windows.  

I suggest to try to find a tool that does all of that so you dont have 6-8 windows open to manage everything.

The Walmart window plastic works well and if you don't have dozens of people crawling on it, will last as long as the house.I understand the tight quarters, but there are some things you should understand about vapor barriers; they don't have to be perfect, a gap here or there isn't bad; and some is better than none.With help, you can open up the floor, which it sounds like you've done some, cut the plastic into strips and pull them from one end to the other.

I would bet the house has high humidity or condensation on the windows.

you could do a brick step-out up top rather than a custom cornice that could be very pricey. it could look nice if you color match the vintage brick or go the opposite and do a contrasting color (like white to match your windows and basement) to make the top stand out. attached are some examples of some top step-outs. the brick mason doing the re-pointing could probably give you a quote for doing the top as well.

They look at the appliances, roof, condition of walls, underneath all sinks for leaks, fire extinguisher in order, smoke detectors operational and working, screens on windows, locks on windows and sliders, A/C filter changed.

@Anson Young its an unusual situation, we are at the point where we can file for the deed but because it's been abandoned so long, there are tons of liens from the city (yard, trash, broken windows) and we have had a hard time getting funded because that title will take 6-12 months to come through.

Didn't deter the intruders at all because they knew nobody was living there and there were tools just sitting around.Even there - I think the culprit was cheap doors (door jambs) and windows.

There is a very small window and specific rules must be followed.