PRS have reversed magnets on the neck pickups when they use the 5-way rotary switch, like on the old Custom 24s. It's so the "split" positions work properly (I don't know if that's a phase issue, or whether it's to get hum-cancelling in the split positions).
I'm not sure if they do the same thing on MCartys, because you just have a normal 3-way switch plus the push-pull coil split.
Anyway, it does sound like they're out of phase. You just need to swap the wiring on the VHII round (so red is ground and black is hot).
Thanks Phil, I had tried it and strangely had the same issue with level drop, but not the thinness anymore.
Well conclusion is that I put back both stock pickups, and although they show low resistance in the middle position, they sound full. I did have a lot of fun playing ... there is something about these McCarty pickups, they sound very big and crunchy, yet airy. But I have bad squealing issues with volume/high gain.
I'll leave them in for now and try with the band, if the squealing is a killer, otherwise I might just keep them in there. In the end they were designed for the guitar, and they do make the McCarty more Les Paul like in fact.