I have a few mixed sets that I really like, but the Riff Raff bridge and SM (AIV) neck really do work together well. I also have an Emerald/AIV Mule set that I like for the more rocky stuff. I have an AV Mule with AIV SM neck too, that is an awesome sound, possibly one of my favourite combinations that is not a real set. For something more heavy, the Cold Sweat bridge and Abraxas neck are a good combination, as are the Nailbomb bridge and Cold Sweat neck.
A combination that I wouldn't have thought of, but which does work well is a Mule bridge with VHII neck. My friend has it is a 62 SG and it sounds great.
BK are very good and they will advise you if you are going down the wrong path. The thing to do though, when you order is to tell them that they are going in the same guitar, and also tell them what guitar.