Sounds like you are discovering the joys of BK pickups
Seriuosly, the Trilogy is a high output single coil and you have it in the neck, I think this is part of the problem, as it will sound way more powerful than a standard strat pickup.
Also, you can check the magnets by holding the top of the Trilogy to the top of the Swineshead. If they attract, they are opposite polarity, if they repel they are the same. If they are
not opposite polarity, this could be why the sound is thinner, as you have the strat 'out-of-phase' sound.
Like Hayden says, you can also try to reverse the black and white leads, but I am assuming you didn't change the Swineshead. Unless you changed all 3 pickups at once?