Looks like you're getting this sorted out. Keep in mind that the foot-switch only switches the graphic EQ and effects loop in and out.
I have to agree with you that the compressor and gate circuits can be troublesome. Unfortunately, they are always in the circuit. The instruction manual says that rotating the threshold knob fully counter clockwise turns off the compressor. From experience, I do not think this is the case.
Even when setting the threshold and ratio to the minimum I can get the compressor light to illuminate with high enough gain and EQ settings. Granted, with the ratio at 1.3 to 1 it's not much, but the manual is misleading in stating that the compressor is off. In Carvin's defense the manual does go on to explain that the gain/EQ/compressor interact with each other.
Since the input gain affects the level that the compressor sees I tend to back off on the gain until I see the compressor light stop engaging -- or at least only when I hit my loudest peaks. I kind of use the compressor light like I would use the clip light on some other amps. I don't think I ever see the clip light for the input gain light up unless I'm hitting the bass really hard trying to get it to light up.
I have been using an R600 or R1000 for at least 10 years, and it has a good powerful power amp (two really!) but the preamp is not for everyone. Like you, I have started using the effects return to run a separate preamp to the power section with good results. Since you are doing this too, you may still want to look into getting a foot-switch. With the foot-switch and a pedal that splits your signal (I use my Boss TU-2 tuner), you can have two separate preamp settings available at your feet. EDIT: If you do it this way, you have to plug a "dead end" cable into the effects send jack or you will be sending signal from both preamps to the power section when the effects loop is engaged. The dead end breaks the normal connection in the effects send jack, saving you the need of an A/B switch.
Good luck!