Sounds like a very good idea to me. Should be feasible with that 3" you have to work with, as I'm thinking you'll need some room for some sort of flange and/or seal in addition the the thickness of the movable roof section. I'm guessing the fan will have to be eliminated or relocated.
I have seen a few things out there. The high being Anderson Mobile Estates that was featured on episode 1 of the Travel Channel's extreme RV series. Anderson Mobile Estates
They build high end trailers for hollywood stars on the movie sets. They build two story trailers where the entire roof section raises several feet to have a full length, full height second story. I am assuming ridiculously expensive. Their entire business is custom fabrication of things just like you want so I am sure they would do it, but take a big wallet. Of course on the other bottom end of the scale would be robbing the roof and lift mechanism from a pop up camper. I'm thinking they would be about the right size for the bedroom section. But maybe a little inelegant for a nice rig like yours. If nothing else I would go "shopping" at your local camper sales and ask the nice salesman to demonstrate raising lowering and securing a pop up so you can get a good look at the lift mechanism, hardware, seals, etc. to see if that sort of thing could be fabbed to work in your situation.
I also remember seeing a full sized toy hauler fifth wheel camper advertised that had just exactly the sort of thing you are describing, it had a pop up type bedroom over the hauler section that raised up high creating a tree house type bedroom for the kiddies up on the roof with traditional pop up type canvas walls and of course the rigid raised roof section. I am thinking most if not all of the height of that bedroom was near or above the roofline when raised, but the concept would be the same. That one had a ladder to climb up into the bedroom. I wish I could remember where I saw it or a brand, but I have no idea. It is out there though, somebody is building it.
I am certain that with the RV industry being in the state it is in, there are plenty of candidates in Elkhart that would jump at the chance to do the work. I think I'd try to find the company making that pop up roof toy hauler, surely they'd sell you the whole assembly and parts to get it done, even if you had to have it installed elsewhere or did it yourself.
Good luck, and keep us posted.