I too have a squealing or whisling noise happenning with my 2006 chevy duramax with allison transmission. Mine does it most in fourth gear around 12psi boost and up while towing or putting my foot into it. It goes away when it shifts to fifth gear. Maybe because the boost drops? I first suspected a transmission noise, but I may have a similiar problem. What bolt came loose on the intercooler causing your noise?
It has made the noise for months. Just notice it a lot more after I got EFI Live and tranny built since it runs harder. I blew the boot loose last week when I took a buddy for a drive. I heard it go "poof" didn't realize what the "poof" was until I got under the truck this weekend to put nerf bars on and saw the loose boot.