Hey Slickrock,
I didn't realize how much trouble you were having with this until I read this thread.
I'll try to throw some reasoning out on the table.
It seems you may have had an adjustment problem early on. When you talked about backing off the pushrod, and the brakes unlocked, that would indicate there was a problem with the mechanical side of things (MC, pushrod, etc.).
You replaced one of the lines last month, and the problem was gone for awhile, right? It didn't return until you flexed out the suspension, which would also work the soft lines beyond their daily use. I'm thinking that there is still crud in the system, or those other lines are breaking down, just like the one you already replaced.
The only other thing I had in mind is the booster staying actuated. Let me try to reason through this. The booster has a valve built into it, where the pedal rod pushes it. As soon as that valve is opened, it starts letting vacuum into the booster to assist in applying the brakes. If the valve is held open when it shouldn't be, it can actually apply the brakes harder and harder until they lock up. Things that normally cause this are pedal adjustment or stoplamp switch adjustment. If the stoplamp switch were sticking at times, it could cause an intermittent issue.......Now, as much as I like my own theory, I think you've disproven it when you disconnected the vacuum source to the booster, which should remove all vacuum from the booster. Still, it wouldn't hurt to check that stoplamp switch for smooth operation.
Hope to see the rig in person someday, maybe on the trail.