Cat 312b pump noise

Hi all
Cat 312b yr 2002 6sw00826
Pump was re-conditioned 300hrs ago approx. Recently taken out with engine to do an engine re-build. Now all back in and running the pump makes noise when operating certain functions. No noise with engine idling and operating all functions. Up revs to 5 and above I get bad noise when using bucket ram in and out and with 1 track. Swing and other track no noise. Stick and boom noise but less severe. That points I guess to an issue with one of the pumps. Its a dual variable piston pump Kawasaki Kv3. I've never heard a pump cavitate but the noise is a high pitch whine.
When holding bucket fully open or closed noise stops??. I know I didn't bleed the pump exactly as instructed but I've got oil coming out of all ports. The oil from the case drain filter is also clear. Could I still have air trapped in the pump? Or could the problem be after the pump. Should I drain down and reprime again. Whats a good method to do this?. Any ideas please.

Are you 100 percent sure the engine to pump coupling is in good shape id assssume it is. Are you also sure a ugly rag or other dothingy wasn't left in the suction line to the pump

Was the pump making that noise before the engine was removed.?

Did you crank engine without starting while bleeding the pump? It doesnt take much to cause pump damage if it was started then you tried to bleed it. Hyd shop recondition pump?