Hiya, :)
I would urge you to re-check the wiring ( including solder joints / splashover at the 3 way toggle ) and the 'offending' tone pot for heat / soldering iron damage to it's track - as I have had the same pickups as you in a Les Paul Standard, a 335 copy - and an Ibanez AF75 - and in all guitars the problem you describe never occured. I could / can always roll the tones to the sounds you describe by about '5-6' on the tone pot.
I was however caught out in a very similar way whe 'transplanting' my Mississipi Queens between guitars, all looked well, but when I replaced the pot(s) all was well. I have also encountered self inflicted short circuits as the earthing braid / star grounding was re-seated in haste. :)
The other option ( which I tend to do for different reasons ) is to roll the volume pot or pots back to 8 or 9 - especially on the bridge pickup if 'blending'.
None of the above is meant to sound patronising, nor does it assume you would not ( like me at the time ) professed to have checked . It's just that my own fault finding improves markedly after a good filter coffee ! :)
