I wanted to give an update and wish I had this resolved. Still looking for additional help and hope the additional photos provide more information as I'm not the most informed on roof/chimney issues. I'm lucky a friend of a friend has a good drone and got these shots.
My home inspector came over and noticed that there's moisture in the walls next to the chimney in the bottom unit and the middle unit, but not the top unit. He felt it's coming from a mix of the poor flashing and chimney top (although he never saw photos of the top and just sent them to him now). Also there is a furnace directly above the 2nd unit near the chimney, but I did not see any water anywhere in the furnace room.
Currently I have 1 quote to add a concrete crown and cap for 1K. Another quote to demolish and rebuild the chimney for 3.2K. I have 2 more chimney guys coming this week. They basically say what they will do, but give no reassurance of what actually needs to be done to prevent the issue without costing more than what I actually need done. I also have a HVAC guy coming Friday to determine if anything is using this chimney and will just remove it, if possible. From these photos, what seems like the best option?
Also it would be helpful to know if I can have any recourse on the licensed, bonded, insured roofer to get money back to fix their issue. It's clear this type of chimney work isn't their specialty. I'd appreciate any advice!