Wow - impressive looking wagon!!!! Well done. I used a GM pump on my 6.1 . It was part of a front drive kit from March Performance coupled with a Mustang rack that was part of the RMS Alterktion kit. I had a lot of pump whine (really bad when turning) but noticed that there was a lot of air entrained in the fluid in the remote reservoir. The aerated fluid got sucked right back into the pump. It seemed to my engineering eyes that the reservoir was simply too small and poorly designed. I consulted with a couple of others and they both suggested a bigger reservoir. I ended up using this one
http://www.billetspecialties.com/assets/1/7/77910_77920.pdf . Notice the tube inside the reservoir on the return side that really helps ensure there is very little air entrainment. Tuff Stuff also send me a new pump with a revised relief valve at no cost. After that - no whine.
This may not help with your current setup - but generally if air gets sucked in (bad seal) or by a poorly designed reservoir - it will whine for sure.
Jim
PS Here is a link to my build. Some info at the bottom of this page and the next.
SRT8CUDA Build