I just replaced my power steering pump the other day and since then it has been a slight hiss or wine coming from it, this was the first one I have done so I was wondering if the pump needs time to break in. The fluid that came out musta been really bad because the fluid I used to flush it was clear...

 

Did you bleed the system after changing the pump? Normally a series of turns from lock to lock.
Some pumps, reman's in particular seem to be noisy, sort of a whiny grind when you turn the wheel.

 

It's not unusual to get a bad rebuilt part. It took three PS pumps from O'Reilly's to get a quiet one. Here's the right way to set up a new pump:

CAUTION: Use Mopar Power Steering Fluid or equivalent. Do not use automatic transmission fluid and do not overfill.

Wipe filler cap clean, then check the fluid level. The dipstick should indicate COLD when the fluid is at normal temperature.

1. Fill the pump fluid reservoir to the proper level and let the fluid settle for at least two (2) minutes.
2. Start the engine and let run for a few seconds then turn engine off.
3. Add fluid if necessary. Repeat the above procedure until the fluid level remains constant after running the engine.
4. Raise the front wheels off the ground.
5. Slowly turn the steering wheel right and left, lightly contacting the wheel stops at least 20 times.
6. Check the fluid level add if necessary.
7. Lower the vehicle, start the engine and turn the steering wheel slowly from lock to lock.
8. Stop the engine and check the fluid level and refill as required.
9. If the fluid is extremely foamy or milky looking, allow the vehicle to stand a few minutes and repeat the procedure.

CAUTION: Do not run a vehicle with foamy fluid for an extended period. This may cause pump damage.