I'll second the idea of Cat and Deso, if you can get out there. The Cat permits are essentially walk-ins, so that's the easier permit to get. As has been said, Cat gives you lots of flatwater on both ends of a day of GC-like whitewater. You can get ferocious winds on the bottom end, which is why you saw motors being mentioned. And it's a long shuttle.
Fall Cat levels are likely to be reasonably low. But one October I did a Sand Wash to Hite, and was cold and rained hard every day before we got to the rapids. That brought it up rather smartly -- maybe 18-20k cfs, IIRC. The good news is that even at those levels, it's possible to scout the most challenging drops, if you feel OK about your water-reading skills.
While your river ability will generally translate, there are some things about long desert river trips that you won't get in those nicely wooded hills and valleys in Appalachia. You might want to take a look over at the Utah Rafters and GCPBA Facebook pages, and the GCPBA listserv -- https://groups.yahoo.com/neo/groups/gcpba/info
-- post there for folks who could act as "consultants" for you.
Hope this helps.