Glad to hear you got both channels back with 'Amp-In'.
No, the relay shouldn't click in and out when switching between Tone Control modes. Did you recap the relay board already?
For the pre-amp, I just had a problem with my stock jumpers on my 1200, where the jumper would cause a low frequency oscillation significant enough to prevent the relay from staying closed. In my case, the relay kept clicking open and closed, like an old telegraph. Do you have an RCA cable to swap in place of both of the jumpers?