The stepups do not have to be that far away.  Depends on shielding, etc.  Inches make a difference.  The main problem was the narrow chassis, forcing the routing too close to the power tranny.  A wider chassis would be ok, or routing the inputs into the front side.  Basically, don't run the low impedance signals right next to the power tranny.  It's a magnetic induction problem, which is why it doesn't show up with 47k loading.  
Think of it this way, 6" or closer to the tranny is bad.  12" is great.
jh