Thanks, Cat. I needed encouragement to get past thinking I might be beating a dead horse.
Had to do a number of things to fix it.. Uninstall Droid explorer to stop the "out of date killing", and something was wrong with the Sony driver. I just got lucky on that one, I think. Replaced it rather randomly with another one the driver update located.
I finally got root with Bin4ry's tool. Then did the update flashing with the custom pre-rooted R5A FW.
I didn't think of trying your method, but if I had seen it sooner, I would have tried.
Any way to confirm that I have the right recovery? I guess it is just an earlier stock recovery that doesn't break rooting.