two weird noises

Okay so I have two weird noises. 2003 A4 B6 Avant 3.0L 6mt

One I have the Jhm trio kit with the crossrod upgrade. I had a flush of the tranny done and when I shift sitting still the engagement is loud. You can hear it. I know the fluid was coming out the fill hole so it had enough in it. Anything else to look at?

Also when I reverse you can hear a whine. I believe its coming from the rear. Guessing maybe fluid change?