I've spent more time working on that board than any other in any of these amps. The circuit is confusing and can do all sorts of ugly things when it wants to. That being said, they do work when they are fixed up.
The basis of the switching circuit is as you figured, Q806 and Q807 ground out either the clean signal or the reverb signal depending upon whether or not the foot switch is grounded. The important thing to remember is that the junction of the two transistor's bases must switch from a positive voltage to a negative voltage. When the bases are positive the reverb is turned off, and when the bases are negative the reverb is turned on.
What sort of noise are you getting? I guess that there could be some sort of signal feedback loop if one of the switching transistors is either open or not grounding.
There was a revision to the circuit that changed three resistors R836, R837 and R848. Does your board have the new resistor values?
As for the question about the RCA jacks, the ground is intentionally disconnected on the send jack. This eliminates the ground loop caused by having a tank with both in and out jacks grounded to the case.