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Intonation issue on 92 Precision Plus Deluxe

I have been borrowing my buddy's 1992 Precision Plus Deluxe, that he's had since 1993, and It's never been setup since. It has a couple of problems that I was hoping somebody could help me with:

1. I checked the intonation, and the E was crazy sharp. I adjusted the bridge almost all of the way to the back, and It got better, but Is still pretty far off. I tried lower the height, but that didn't help, so that leaves neck relief, and the nut. The neck doesnt look that bad. What do ya'll think?

2. The A string is really quiet. I tried to adjust the inner screws on the P bass split coil up in the center, but no real change. This thing has the active lace's on it. Have they been known to go bad under one string only?

Thanks for any insight.
 
Thanks for the response.

I probably should have mentioned that the strings are flatwound(if that makes a difference), and they are only like 3 months old. I guess that "setup" has many connotations, but I meant it hasn't had a check up with a professional. I changes the strings, and made some minor adjustments, but haven't touched the neck. I'm a little hesitant to adjust the truss rod, b/c it's not mine.
 
They(the strings) seem to be set well. It's just like I've run out of room to move the saddle back any farther. I guess if I bowed the neck some, that would lengthen the string a bit more, but I've read that there's usually not much of an intonation change from adjusting the neck. What about raising or lowering the saddle.

anybody got any ideas on the quiet A string? This thing has the P Bass split coil, and the jazz bass one in back.
 
I have had the same problem when I first used flats. Messed with it and messed some more. One day I backed my E saddle all the way towards the nut, shortening the string. Then I intonated at the 12th fret, disregarding the open string or 12th harmonic. Once it was good at the fret, the harmonic and open were bang on!! The position of the saddle was now well forward of the tail! Can't explain it but that's what happened. Now I'm in the habit of intonating the 12th fret first and then checking the harmonic and open. Try that.

Now, just the other day I put hipshots on my VM Jazz. 28:1 ratio. So precise they are that when an open seems tuned, the 12th was flat. So I tuned the 12th first and viola, the open and harmonics were bang on! All I can figure is it's my tuner not being very accurate plus added harmonic content of the longer open strings???