Great thread.
I have had a few Wagoneers over the years and worked through all the same problems you have been having. It brought back a lot of memories.
One thing I would suggest is consider a stock motorcraft 2-bbl carb from a Wagon, J-truck, or v-8 equipped CJ. You give up a little power, (but Wagoneers aren't exactly hot rods to begin with), but it is soooooo much friendlier off camber. I had an edelbrock perfomer for years, good on the street, but off road all it did was run rough and catch on fire a lot. I put a motorcraft on it, and suddenly quit lusting over fuel injection. The time I lost between 0 and 60, was more than made up for in the reliability and lack of frustration off road. No more stalling on hills or bumpy roads. No loss on the low end, and not much loss under hard acceleration. But, it sounds like you have a better understanding of carbs than I do, so take that with a grain of salt. My wagoneers are gone, but I still run that setup on a '72 CJ-5. The only time I miss fuel injection is while it is warming up on cold mornings.
I would also second an earlier comment about a spare fuel pump. Electric is much better and definitely the way to go, but I have replaced three of them on the trail. My brother even plumbed a backup next to his primary and could turn some valves and move a ring connector to switch over to the backup. Ironically, once we went to all that effort for a spare pump, he never had another problem with the primary.
Great truck, and it does my heart good to see someone enjoying it.