Am I understanding properly that all these noise issues are associated with the 'pure' analog inputs?

Or more to the point, does this noise problem affect the 'normal' A->D->A analog inputs and D->A inputs? If not the TAP solution is what I'll look into, but if the digital side is also showing problems I'll need to look elsewhere. Maybe 1066+TAP????

Also, is the noise issue a gain structure problem I could fix with adjustable gain on the amps? I will have adjustable gains there.