What guitar do you have, and what pickups does it have at the moment? If it's two humbuckers connected to a 5-way switch, you won't be able to get exactly the same wiring options, because the Mississippi Queen is a single-coil (but you could get a tapped version, which would give different options).
The thing about not getting clean sounds is just nonsense. The MQ will give you great cleans and so will the NB as far as I know, especially with a coil-split option.
As for Duncans or DiMarzios, they may or may not suit you better than the NB/MQ combo - it all depends on the actual models you choose. All three companies have big ranges of pickups.
One thing's certain, if you pick the right BK pickups for you, they'll be at least as good - and almost certainly better - than anything from another manufacturer.