The den had a closet and full-sized window.

People forget, people lie.

It may be petty for the tenants to hassle you if they know the property is for sale, but a courtesy that I employ when selling an occupied property is to inform residents that while we'll try to conduct all showings (exterior and interior) on set days during a certain time window - sometimes person's may stop by and walk the property without my advance knowledge.

Looking to start with window installations next week as a trial.

The den had a closet and full-sized window.

Have the tenant talk to the neighbour and see if they can come up with a compromise-eg if they are smoking can they (the person smoking) keep the windows and doors closed? 

CHECK,Boarded-up windows?

good deals are not easy to find. if they were, everyone would buy them. just keep looking and don't forget the basics. you're also in a HCOL area.

Should we invest in replacing the central A/C unit, or would window units be acceptable for resale?

For example, flooring, drywall, and window installs are tasks you could probably find other contractors or even handymen for without needing licensed trades.Since you’re doing materials and design already, use your time to line up what’s needed before the trades get there—be the “project manager,” not just the labor.