As far as the botched duct, there is different types of duct you can install so it doesn’t hang so low or impede a low basement ceiling. With duct work it really needs to be as direct as you can, the more 90s in a run to a register off the main truck really lowers the airflow.
But it can be ran in wider but shorter duct so it doesn’t hang as low, they make oval pipe for diffuser runs that keep clearance under at a maximum, easier to hide in a drop ceiling etc.
As far as the flue being angled, it has to be that way, flue pipe condensates a good amount of water, that water has to travel back to the furnance. PVC handles water better than metal but if slopped enough, should be ok for a while, more than 10 years, maybe 30 idk.
Trane is ok, I’m not a fan of them, they are old technology, they haven’t updated there equipment as much as carrier and Lenox has. My fav is prob Rheem, they are simple to work on, they seem to be really reliable and just work. Lenox 2 stage furnance with a variable speed blower is nice, it ramps up slow, doesn’t create duct work flex, runs at the speed that’s needed vs a set speed.
But I have a love hate relationship with Lennox, every furnance that stumps me and I call hateful names to seems to be a Lenox every time lol. Idk why
If it was my place, I would do the work myself but I would prob install a Rheem HE furnance paired with a heat pump and topped off with a smart stat, I have a Honeywell 8000 on my wall, I can set parameters for the heat pump to run till the outdoor temp gets to 32, after that the furnance runs, saves on utilities and no colder drafty type environment inside. I guess manufacturers are saying to run heatpumps down to 0 degrees, at some point you are trading dollars of savings for wear and tear on the equipment. What that threshold is idk. And I would most likely do a concentric out the back of the house. It’s not a eye sore, not something people notice and much easier to do vs roof in some cases, I have mainly put in roof concentrics.