Glad I saw this thread. I'm still working on my organ and feeding diagram for the Andalite to go with my anatomy sheet for them, and I have a feeling that it was someone from this place who asked me on deviantART whether I was going to do one for the Hork-Bajir as well.
Anyway, my two cents on the topic of Andalite anatomy and feeding: in my head canon both hearts are located in the humanoid torso of their body, and their lungs in the other, mostly to make it look less like two torsos of different earth species (human and deer) pasted on top of each other and their organs combined. Their wind pipe would be larger (extra room because the esophagus is located elsewhere) and strengthened with extra cartilage, allowing them to breathe in more oxygen with each intake of air.
The two hearts would be larger because there's more space in the ribcage (no humanoid lungs) to be able to pump blood through their system faster. Their actual lungs would be a little larger as well because again, extra space, no deer heart.
I figure that they would have some kind esophagus traveling up their legs, though thinner than a regular one, because they have four of them and there really isn't that much space in a deer's leg, especially in the lower part where the metacarpal bones are located. It'd be located close to the bone, following it up, and be protected by a layer of muscle. A lot of people mistake the shoulder area for a deer/horse's upper leg, the actual upper leg for their lower leg and their lower leg for what are essentially hand/feet bones (metacarpals) and fingers/nails (hooves). The upper and lower leg have more muscle layering, so it'd be more protected, but the rest is mostly bones with tendons and smaller muscle groups here and there. An esophagus located there wouldn't have a lot of protection from kicks to the leg.
Either way, it'd travel further up, along the bone of the lower leg and then into the abdominal area, beneath the shoulder joint. Same principle with their hind legs.
Still with me? XD
As for the stomach, I'm not sure if I'd give them a four chambered one simply because they're not earth animals. For all we know they have three, five or even eight chambers. I do think that they'd have a strong stomach and powerful intestines to digest their food with.
Plant material is tough stuff to digest, and it's pretty much impossible to also add teeth inside their legs. They also wouldn't be able to swallow stones large enough to help grind grass once it's insides their stomach.
They'd need some kind of mouth and they should be able to close it so they're not constantly eating 24/7. They're even-toed, so I figure it's like some kind of sphincter located just between the hooves, very roughly textured on the inside (like a cow's tongue) to grab the grass while they're running and push it up their esophagus.
I haven't thought about the location of the other organs yet, but this is kinda how I see it. I haven't really spent a lot of time on it yet, there are still plenty of kinks that I need to work out.
Like I said on the actual Andalite anatomy sheet I'm no anatomy major, I'm just a nerd and I'm bound to make mistakes no matter how much research I do
Though glad that if and when I do the Hork-Bajir, they won't be so complicated to figure out.