They definitely patrol Deso in the fall...at least until it freezes. Not hard to get a permit though, and its only $25 per person. Lodore permits aren't hard to find in October and November either, but it gets cold. If you want to check out the canyon, I have a trip I posted about October 27th through 31st in Lodore.
The section between Dinosaur National Monument and Deso is not supposed to be all that nice to go down. Minimal camping spots, entirely flatwater and not much to look at beyond some cool birds. The few accounts of people I've heard do it say its only worth doing to say you did it.
The section above Lodore sounds mellow but nice. Sounds like the section between Deso and Stillwater is kinda monotonous too, but not as bad as Splitmountain to Deso.
I would definitely pick a time of year that is NOT bug season.
I'll be honest as say that I could see doing this trip at some point too. I think I would be tempted to use "the black oar" for significant sections of it though. You can't bring a motor through Dinosaur, so you'd have to arrange drop off in Jensen (or do a good job hiding it). You'd probably want to restock a bit anyways. Maybe work a deal with River Runners Transport for a combo deal of the Lodore Shuttle followed by the Deso shuttle from their office instead.
However you do it, a trip report would be awesome.