The XT1 is not near as fast as a D4. In good light with the right lenses, the XT1 is almost as fast as an EM1 or other modern m43 body (again, with the right lenses). This is a real accomplishment for Fuji. In low light, though, it slows down and the Em1 really doesn't. On the whole, for S-AF, I'd say that Fuji has finally reached the point of "fast enough". It's not the world beater Fuji claims, but so what. Once you're at a certain speed, it's all just kind of game playing whether one is faster than another. M43 has been at this point of "fast enough" since the GH2 in 2010. It's gotten better but not in a way I'd say matters. Fuji is just getting there and still has some work to do in lower light.
Once place where almost every reviewer (other than Steve Huff) seems to give Fuji a real edge, though, is in tracking AF during burst mode shooting. It's evidently the best mirrorless camera for this, other than the much smaller sensor Nikon V1 / J1. And this is after the EM1 was supposed to have made big strides in this area. I don't use this mode really at all, so I can't provide any independent verification on this, but there seems to be an emerging consensus out there that Fuji got this really really right. I haven't seen anyone compare it as on par to the D4 though...
I can't speak to the K3 - I'd assume a DSLR focus system is still marginally better, at least in lower light and at tracking, but I think this is somewhat lens dependent and I don't know anything abut Pentax lenses except that they sure seem to pack a lot into a small space!
-Ray