For the record, I was able to bring the intonation to a reasonably good level. It's still not perfect due to the banana neck this vintage instrument has developed over the years, but it's not so bad now.
In the time that I couldn't take care of the intonation issues, I was able to go through the recordings with the slightly flat tuning and laid down pitch perfect tracks.
Somebody mentioned using Melodyne... I did that too and was amazed at how well it worked. Virtually no sign of tone degradation. I realize it might be a good habit running important bass tracks through it anyway, just to be sure...
Thanks everybody for the input.