The ducts are in the ceiling and there is no attic to access them.

Is this the best placement or could it be on its side and have the ducts run underneath the house? 

I've seen a ton of amazing deals on paper, but when I visit I notice the house is held together with duct tape and it turns out they have no occupancy permit to be a triplex or whatever.3) The fact that it's been on for 6 weeks does tell you for some reason investors in the area are not interested - because in my experience most multi-units have investors crawling all over them on the listing day, but that could be a variety of reasons and honestly I've seen many similar deals in the slopes over the years - only way to know for sure is go see it. 

What’s the brand and color of the wood Look flooring and tile you like?

If it's a neutral color and you can get away with just getting it cleaned that's what I would do.

I chose this option because I would never have to worry about a furnace or maintenance on ducts etc. 

If it’s a gut job, then I usually go semi modern with new materials.Keys is to stick to one theme throughout and work within he same color pallet.

The tree has caused extensive damage; beams are coming down through the ceiling, the AC is leaking, duct work is coming through the ceiling, roof is damaged, etc. 

We have that first thing you posted, except that it was a professionally installed unit that was manufactured and it looks nicer than just open duct work as the area it is used in is a finished bedroom in the basement.

also, I'm told after Tenants move out with Cats to do all the Remediation work, Remove all Carpets put down new flooring, repair and clean all surfaces including air ducts for heating and air. to call an Indoor Air quality inspector and get units certified as Allergen free.