Incorrectly set or dodgy load sensing valve can have an effect on braking performance.
Insufficient or intermittent vacuum will definitely have the effect on braking pressure application as pressure loss/assist will affect the outcome.
Incorrect master cylinder will affect braking pressures. I wonder if you have correct one!
Finally standard Y61 brakes except on 4.8L engined ones are chit! Generally softer pads will improve braking performance but wear out quicker.
4.8 L brake pads (Nissan OEM) will fit to ZD30/TD42 brake calipers and they're an improvement.
Regards