Power steering noise after rebuild

My 99 4x4 2.7 tacoma started making a whining noise after I replaced seals and bearing on the pump.
It was quiet and worked great with no issues. The only thing was a slow leak from the pump shaft seal. When I took it apart I decided to replace the bearing as well. I drove the car without the pump on for about a week waiting on the parts which caused the rack to lose all the fluid it. I replaced the seal and bearing, assembled the pump and put it back on the car, filled it with fresh ATF Dexron III started the motor and now the whining won't go away. I have driven it for 50 miles. Bleed it a few times (steering lock to lock with tires off the ground) still makes the noise.
Question is, why a good pump died in the process? Can driving with no pump and fluid damage the rack?
Thanks

RB

 

I think you will find a fine screen in the bottom of the reservoir and it will be plugged up with kurd.

 

Forgot to mention that I have already checked the screen and it looks clean. It even has a tear in it so it can not hold the fluid back in anyway.

 

maybe the system needs to be bled.