Did you set the Rotor & Slide clearance correctly when you rebuilt the Pump?
The Stem on the end of the Pressure Regulator Valve will keep the Low/Reverse Boost Valve inplace, keep it from going too far into the Pr
. Reg. Spring when assembled. Needs to be assembled from the bottom of Pump. If it was assembled with the Pump upside down the Low/Rev boost could've been cocked out of place. This would cause problems but, I doubt it would cause the clacking noise.
Most recommend 1/8" - 3/16" clearance between TC & Flexplate before sliding it forward. More than 1/4" requires Shims between TC & Flexplate.