How many turns out was the airscrew with the 42? Seems like the 45 at 3 turns out would be as lean as the 42 all the way in. What about your needle? Stock? Stock position?
Lugging around at low rpm is the easiest way to make an engine ping, and it if runs good everywhere else and only pings then, your jetting must be pretty close. I'd look to fine tuning like raising the needle (put the clip on a lower groove) one notch or turning in the airscrew a little. Weather conditions can also be a factor. If you were well jetted for poor summer air and were riding on a cool day with good air, that could have contributed.
Re: brake pads, mud is much harder on pads, but the stock KDX pads usually are pretty long lived. In extreme conditions, 100 miles might be about right, but you should normally get much better life than that on the stock pads. If you are unknowingly dragging your brakes (pedal to high?) or have some air in the system (seems common on Kawasakis), that could certainly shorten pad life.
FWIW, aggressive compound aftermarket pads will wear much faster than the stock compound. IMO 100 miles in the mud would be about the best you could expect from a real aggressive pad. The only time I put race pads on my KDX they wore out in about 2 hard trail rides (approx 120 miles).