It sounds like you are doing all the right things to track down the noise.
One thing to be aware of is that if a module is dumping noise into the system that same noise can present at the output of other modules!
This can lead to a cascade of noise build up, the one problem becoming more amplified as more patch points are connected to the outputs.
The first time I encountered this it drove me crazy until I figured out what was going on, it just so happened that I had one module with a screen that was generating noise (as they do) right next to another module that was very prone to picking up noise! Who knew!!??
Also, I am sure you know this anyway, but for those who may not, check your gain staging.
Finally, some proper analysis tools can help enormously when tracking this kind of thing down.