Good to hear from you again!
The box that I am looking at using is ten feet tall, so my thought is that if I put the shower outside of the frame rails I can drop the floor (in the shower) by six inches. This gives me 6'11" clearance in the shower and I can still fit a bed with three feet of clearance above the shower.
Is the 10' height the outside or inside dimension? By the time your add shower pan, plumbing, structural shower ceiling, etc., you'll have less than 36" left for your sleeping compartment. This assumes you're going to collect your grey water. My box is 9'8" high.
Now I am looking at a ten' wide box, so that may be different for you, but if you can drop that shower down you might be able to put a bed above it. That is a lot of space above your current bathroom set up that could be used. Heck you could drop much of the set up down, even the toilet and floor around it.
I'm assuming you meant height. There is some space above (9.125" above the frame of the 6'8" door frame), but not much, and it will be used for 1) a low profile propane furnace; 2) ducting for the A/C unit and the furnace; 3) various and sundry wiring. In fact, it is actually a pretty tight squeeze.
The grey and black water tanks are directly beneath the bathroom floor, so I can't drop my floor at all. In fact, I almost raised floor in the forward 7' of the box so I could increase my waste water capacity (60 gal, and 30 gal).
You already mentioned, in the mock-up of the interior, that you understand the concerns about not being able to slide out your beds. I would just be very certain of that. If you can not, for some reason, slide out the slides, will you be able to still cook in there? I mean if, for instance, something breaks (as you said untested) that would prevent your slide, heck stuck in the middle of nowhere third world country might be a bad time not to be able to use your galley. Hope that does not come out as harsh, not at all intended that way, just thinking out loud.
If you think that is harsh, we need to trade jobs! Fire at will, that is what these forums are all about. All three slide mechanisms have manual override, however, the galley is perfectly accessible with the main slide retracted, and the table can be dropped to form a large bed when the slide is retracted. Finally, this rig is probably not going outside the US except to Cananda, and perhaps Baja. I would've chosen a different chassis, since the Topkick/Duramax doesn't have the type of international support required for extended cross-border trips. However, since the camper is detachable, it would be possible to mount it, and the matching subframe on a different truck. Before that happens, I'll have plenty of time to test out all the moving gadgetry and see if it's worthy of international travel.
On your pop-up. I have thought about Jay's Ecoroamer a lot, and having seen it, and watched them putting it up and down... I think that I would have taken the pop up and made it bigger. Theirs is a hinged idea, I would have used a straight up box but moved the rear end out into the camper far enough that the hanging portion would not be in the way. The reason I say that is that, in my mind, it seems too easy to foul the way it is, and too easy to get crap inside the camper in a wind or rain storm. With four solid sides that all go up and down at the same time you get the head room but still keep some structural integrity. Again, this is just my personal thoughts, with no practicle experience to back up my thoughts.
By the way, if you have not written a PM to jayshapiro, I would suggest that you do that. Ask him about his lift roof, what he thinks of it, what he thinks of your idea, etc. He is a super guy, and can give you some great insight from his experience.
On the pop-up, I'm still tweeking the design. I share your concerns but I'm not too worried about it- after owning commericial RV's, I'm no stranger to "fouling"! I actually met with my engineer buddy today to go through some fine tuning for both the slides and the pop-up. He's very smart and skilled and his suggestions will show up either in illustration or the actual build in the coming weeks.
I've pinged Jay a few times but haven't heard back, which is fine. Sounds like he's out enjoying his adventure with his family, which is what he should be doing. If I'd gone through his build for over two years, the last thing I'd want to do is get pummeled with questions for years after. His postings have been a huge help to a lot of us, especially with the degree of detail and openess. I'm just grateful that everybody on this board is so willing to share their thoughts and ideas.