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Comments
Whichever of the four pickup conductor wires its manufacturer's instructions says should be grounded goes to the same DPDT terminal as the switch's -ve/ground output.
It is possible that the aftermarket humbucker will turn out to be reverse wound or reverse magnetic polarity relative to the stock single coils. Correcting this will involve reconnecting all four colour coded conductors at the mode switch.
The Yamaha single coils are unbranded single wire and braided ground. Can I assume that the middle pickup is RWRP?
If the Yamaha single coils, selected together, reject hum, the centre position pickup is RPRW with respect to both the neck position single coil and whichever coil(s) of the bridge pickup operate(s) when the bridge and centre pickups are selected.
For visual confirmation, invert the Pacifica scratchplate. I would expect the ceramic bar magnets under one single coil pickup will be painted whereas the other will not. The one with the paint is RPRW.
In all frankness, I doubt that the Boo-hueng shredtastic humbucker is going to be a great improvement over the stock unit. My sincerest recommendation for a Pacifica is the Seymour Duncan Custom 5. Second choice; Tonerider Generator or TRH-3 Octane. (Check your polepiece spacing before ordering.)
I already have another Pacifica with a Custom 5. The Epi pickup is unusual in that it is a low wind 9.0k ohm and it came out of the stock Kramer after replacing with a hot ceramic to make it more shredtastic. It did sound sweet in the Kramer, just not what I wanted in that guitar.
The stock G&B pickup in the Yamaha is bland so I am thinking the Epi pickup might give me a more vintage vibe.
Will have another look tomorrow night.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
@Funkfingers thanks for your comments. I wouldn't have thought of the phase issue without that. Wis duly awarded.