So the bunk is situated as seen in the picture below. The bunk has a 2x2 wood frame rectangle with (eventually) two 2x4 cross pieces in the space that isn't supported by the cabinet. On two sides, it is glued to the wall and screwed directly into the aluminum studs. The free side has some bending resistance due to the "railing" that you can see. The bunks are nice 30x75" mattresses. In Canada I can buy what they call narrow twin mattresses from zinus on amazon that are memory foam, I assume they would be available in the states too. So that's what I have for the bunks. There is only one complaint about them so far, and that is that the queen bed underneath it is a bit annoying to get out of the bed at night if you are the one further in. Minor complaint in my books considering what we have accomplished, plus my wife is usually the one getting out if anyone is, so she will probably just sleep on the nearer side.

As for the toilet. I'm pretty committed to the black tank toilet combination since I've bought both, and neither are returnable at this point (and cut the hole in the floor), but I did briefly consider the composting. It sounded like something that would be more complicated for my littles to manage, and also those toilets are so expensive. More than my toilet, black tank and plumbing combined.
Thanks McDave for your insight. So you think its better to go behind the axle with the grey rather than further up front. I guess I should try to figure out what my tongue wait is currently with all the gear under the queen bed in the storage, and the batteries up front. That might clear it up for me, because I figure my wet weight will be around 2500 lbs.
One other question for the readers. I'm seriously considering going with a rope & pole awning as opposed to bag or the current regular RV awnings. Advantages in my mind is big cost savings, less holes in the trailer (potentially no new ones as I think I'd just jbweld the awning rail to the top trim (which itself is screwed in, so its still replaceable), and flexibility in the size of the awning. Most bag awnings aren't big enough for me, and RV awnings would have to fit around my windows. How long does it take to attach one solo if you have one?