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Problem after upgrade, re-string and set up

Hi guys/girls, I have a little problem with my recently upgraded bass that has me stumped. I'm hoping someone can offer some advice.

I wanted a lefty Mustang bass, however no-one makes reissues, and the originals go for a lot of money. My choice was to go for an SX 3/4 scale (short (30") scale) P bass copy, and spend some money upgrading it. I had my tech replace the pickup (with a new Wilde/Bill Lawrence P-46), pots (CTS 250K reverse audio taper), jack socket (Switchcraft), wiring, and pickguard. I asked my tech to install a series/parallel switch on the pickup (he followed Bill's circuit diagram), a set of Rotosound 77 flats, and do a setup.

Got the bass back last weekend, and something's not right. The E string is very hard to tune - the pitch wavers a lot, and emits an odd frequency as you bring it up to pitch. When plugged in thru the amp, the E string has a strange sound - not at all like a standard note from an open E. Fretting on that string, particularly high up the fretboard, the notes sound flat and honky. A similar problem exists on the A string, although not to the same extent.

I don't have the knowledge or experience to solve this, although I'm wondering if the problem is a dodgy string or strings, dodgy pickup, faulty wiring, or a combination of these.

Any advice will be appreciated. Cheers.
 
How high is the E side of the pickup relative to the strings?
That's my question too. I'm betting it's "Strat-its": when the pickup is too close to the strings, the attractive force of the magnets distorts the string's vibration, causing it to sound "out of tune with itself."

To test, lower the pickup as far is it will go and see if the problem goes away

If the pickup is not designed specifically for a left-handed bass, it could be that the pole piece heights are inappropriate for a lefty bass setup.
 
Good detective work guys. The best way I can describe the sound of the open E is that there's other frequencies apart from the fundamental - it sounds like there's some sort of modulation or weird, discordant harmonics going on as well. The tuner needle goes ape when i'm adjusting the tuning on that string, and it's very hard to find pitch. Hitting an open E when plugged into the amp causes the amp to freak out, and this is at low volume.

My tech is very good usually, although he did say that he had a cold and his ears were blocked.