These threads take on a life if their own, don't they?
Setting it up now, my first impression is that, even given the issues noted, the build quality of this bass is great. Rock solid. Much better than my Japanese Aerodyne (which also had misaligned pickups). After putting on some old LaBella Jamersons it actually looks better. I gave the truss rod a half turn before putting them on because of the higher tension, and when putting the neck back on put a little more sideways pressure on it. It seemed to help. Next time I have it apart I'll give the truss rod another eighth turn, but it's close enough now. With the heavier strings the intonation is way off. I'm filing the nut on a couple high strings, that will probably help with the intonation. The nut slots cut close to the side don't bother me anymore, if it becomes an issue I can buy a precut American P nut for $12.
A couple interesting things, you have to loosen or remove the neck to adjust the truss rod. Inconvenient, but not a big deal. And there's not an Allen head anywhere on this bass. I suppose to be accurate to the original 50s bass. And the tuners are reverse. I'll take it to an open jam and watch some of the other players try to tune it.
I no longer regret selling my old P, I see a long relationship with this one.
Thanks again for all the input!