Well, after another four hours of working on the NSX, I'm kind of stuck. Somehow I managed to tighten a nut with stuff attached under it slightly incorrectly, in such a way that I now can't get the socket back on the nut to loosen it. Lovely.
I ended up having to take the front cylinder head cover off again so I could see the cylinder TDC marks on the timing pulleys. The real work (adjusting the valve clearances) went pretty smoothly. Like the front, the rear cylinder bank had many misadjusted valves, mostly too tight.