Ok, I finally got everything drilled associated with the aft skins. And most, but not all of the deburring and dimpling.
I did lots of futzing with the stringers to get them aligned fore and aft (including changing the forward ends) and lined up with the small pre-drilled holes in the bulkhead tabs.
I got the skins off and cheated on the drilling of the F-707B clip to the F-707 bulkhead. I couldn't get good access (or eyes on) to match drill the clip from the bulkhead holes. I did trace the clip with a sharpy while the skin was on so I could get it all lined up and clamped to drill.
I got through some of the deburing and dimpling. Still need to do the skins.