A really well written account of a ride gone wrong. The OP has been very candid about his mistakes and has combined his account with an open invitation for others to contribute wisdom.
It's clear that he is someone who does actually think things through very thoroughly, and some of what went wrong was just bad luck rather than bad management.
As owner of both 1200 GS and WR250R, I would most definitely have gone with the Yamaha for a ride like this. I'm a big-bike guy but I know (from bitter experience) it's a lot easier to get the Yam out of gnarly spots than the GS.
And all I'd say about the need to cover large amounts of road miles with ease- one of the best road rides I've ever had was a 200 mile run before lunch- on the Yamaha. Try one.