The current windows are super old and need to be replaced, I just don't know where to start.

The new rental has a modern kitchen, new appliances, LVP flooring, new central air, LED lighting, new window, paint, texture, etc.

Recently in my quarterly visits I like replacing the hvac filters, run some diluted chlorine down the ac drain line, the water is very hard so I recently started running some drano down the lines.

It sounds like you have replaced all the big-ticket items so there shouldn't be much else to break. 

I suspect it might be allowed for me to reuse most of the boxes, outlets, switches, and lights, but would likely have to replace all the wire that was pulled behind walls as well as the main panel.  

Glue down is easier to replace a single piece, so that is what you find in any commercial setting. 

They have to charge for their time.Also assume that all systems are going to need repair/replacement.

What you really need to do is look at all the items in the property that need to be or will need to be replaced in the coming months/years and figure out how much money you need to set aside every month. 

Is it livable, yes, but definitely needs to be painted and was thinking about replacing the old flooring with new vinyl plank.

If the floors are brand new, I probably won’t allow pets, but they have been around for a while and I know I need to replace them soon I will allow dogs and cats.