Hi, I have exactly what Twinfan describes - a Japanese 62 (the "non-export" version) with all the electrics replaced with BKP stuff. It's a killer guitar.
I went for ITs, but 38thBeatle's posts over the last few months nearly swayed me to Apaches. I believe that the Apaches would be more versatile than the ITs, but I was surprised to find the ITs are actually pretty versatile themselves.
I went the IT route because I wanted a grittier Rory Gallagher sort of tone most of the time. But with cleaner amp settings and the volume rolled off on the guitar (and the right attack from the fingers etc) they will happily wander off into the territory that I believe Apaches cover more naturally.
I might be wrong, but I'd ask which tone do you want to use most of the time? If it's "Gritty strat" like Rory Gallagher or others - then I'd choose ITs. If it's "Classical bell-like strat" - then I'd choose Apaches on recommendations from people like 38thBeatle. As far as I can make out from the clips I've heard, Mother's Milk might do something in between.
Bottom-line though, I don't think you can go far wrong with BKPs. My ITs replaced stock Texas Specials. I like the TSs, but I prefer the ITs in this guitar. The guitar just seems more versatile, expressive, and is even more of a joy to play. The TSs are in old Squier now. I may eventually get Apaches as well and swap the ITs/Apaches between the two until I get the best out of both.