Ok, when removing the pump(s), are you taking the timing gear and housing off of the engine at the same time? That could be some of the problem, if the timing gear is not replaced correctly, but it should make the engine run poorly (if at all), not break stuff. There are 3 bolts that hold the pump shaft to the timing gear. They should be tightened to about 15- 20 lbs/ft of torque. There are 3 nuts that hold the IP to the housing, are they tight?
I am thinking the breakage may be from misalignment, but am not sure where. IP housing? Loose or tight IP shaft bolts? Are you doing any adjustments to the IP for turbo performance?
High mileage will affect performance and oil consumption, but should not break IP shafts. 500k miles is a lot, even for one of these engines, but not unheard of.