One other thing of note is that I believe the inductance issue the amp was creating with the pre-amp due to being stacked directly on top was affecting the sound negatively with all sources, not just phono, which is where it was most evident by the low level hum with the phono section.
Everything sounds much cleaner and more detailed now regardless of source since I put some distance between amp and pre-amp.
My suggestion would be for anyone who has an amp stacked within 12-15" of a pre-amp to consider separating them further and see if there is a difference in sound even if there is no clear audible effect.
I learned a good lesson from this and am now considering beefing up my physical location of components to put more distance between each just as a safeguard.
This experience makes me more cautious regarding receiver and integrated amp designs than I had been prior. There can clearly be issues locating other electronics near high performance power amps that have to be addressed effectively in integrated designs. The impact to the sound may not be clearly audible untill the proximity issues is addressed, which cannot be achieved through physical separation of individual component circuits in an integrated design as can be with separates. The cost of building the integrated in a manner that properly addresses this must be relatively expensive I would think compared to the simpler solution of just providing adequate distance between separate components as needed. Even with separates though, build quality could be a big factor as well in regards to how close pieces might be placed to each other safely without sonic impact, but the safe thing to do is probably to just keep things well apart if at all possible.