Adding a separate system for the 2nd floor and attic

My parents house was built in 1935 with a gravity hot air system. In 2003 the previous owners put in a 90+ 115,000 BTU Amana furnace which was not zoned on to the original duct work before they sold the house. About a year later when my parents bought the house, the had problems with the 2nd floor being 10 degrees short, as the thermostat was on the 1st floor. They had the system zoned between the 1st and 2nd floor and had most of the supply duct work in the basement and crawlspace replaced with flex duct, up to where it went up into the walls.
The bonus room / attic has a 8,000 BTU window unit, plugged in to an extension cord (yes I have told them about it being a fire hazard).

Both systems run excessively in the summer which does not help my parent's electric bill. The duct work for the 2 lower floors is a ramshackle. When our AC is on in the summer the basement gets freezing, (like down into the mid 60s). I have pulled off some of the grates on the 2nd floor and pulled out a ton of plaster, I cannot imagine how much is left the them that is out of my reach. My parents have decided to finally do something about the HVAC.

We all sat down, talked and drew up a 2 phase plan, so we will not be completely without HVAC while we tackle this project.

The 1st phase would be to install a new furnace an AC in our attic eves, for the 2 floor and the finished attic. We agree that we would preferably have gas heat and not a heat pump. One thing that I am not so sure about is weather it would be a good idea to put a 90+ furnace in an unconditioned attic, in a 90 year old house. I have heard about problems with them freezing. Should I suggest they get a 80+ in the attic instead? I am in Durham NC so it does not get very cold here.

The 2nd phase would be to replace the now over sized Amana furnace in the basement with a smaller 90+ unit sized just for the 1st floor and replace the duct work. We would also add a couple properly sealed cold air returns.

My mother has considered just adding a mini split just for the bonus room and not touching our main system. I don't think that this is the best option sense the main system is in such poor shape and almost 18 years old. I also think my mom will want to keep the old Amana furnace until it dies even if it would now be over-sized, although it is already zoned. I am not sure about whether it would be worth running the Amana for a few more years of if they should just put in a new properly sized unit for the 1st floor.
Could install the 2nd floor system but Amana with both dampers open but only have the first floor thermostat and have it help somewhat on the 2 floor during the day, until it needs to be replaced?
my mom tends to turn off the 1st floor before she goes to bed.

What are your thoughts I can post some pictures if need be, hope this is not too long of a post.