As far as the no start problem goes, I had a similar problem on the trip with my brother last year. When we limped it back to the house, it was clear that the R/R was toast. You've already swapped those out, and presumably tested the Honda R/R.
The stalling you mentioned is also reminiscient of how my 550 was acting when the R/R was going. When the revs would drop below 1000 +/-, it wasn't putting out enough current to run everything, and it would die. A simple bump start would get it going again.
The battery that was in my 550 ended up boiling dry when the R/R fried. Even though it still charges, it is not a long-term solution. In fact, it is the first thing to replace on my 550 this summer (I chose to not insure it this year because I'm not riding enough to justify having two bikes on the road)
Did you replace the battery after the R/R?

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