I've has some time to play with this some more and mpaquette comment makes perfect sense as a fix. I'll try to determine which caps are the problem and try the fix over the weekend, hopefully with some pictures. If someone could give me direction on which caps to focus on that would be very helpful.
Looking at the unit i'm seeing 6 470uF electrolytic caps around what looks like 5 voltage regulators. I was expecting to see the nice mushroomed tops but no luck. Are these the caps that need replacing? some of the numbers are C136, C219, C145, C133, C132, and C120.
I actually took the time today to pull out the main board and find out what voltage measurements i should be getting. Luckily Line 6 put a nice set of test pads on the bottom of the main board and indicated what voltage you should see at those locations. What i found is that my +20 and -20 volt signals are showing somewhere around +-13V and what should be an 8V source is showing 3.13V, these are feeding +15V, -15V, and 3.3V regulators. I'm actually surprised i'm not finding more issues with the unit other than the instrument inputs. Surprisingly the regulators are all outputting what they should and my theory is that they are able to do this at the sacrifice of current and the instrument inputs require more current then the other inputs to operate correctly. This then starves the high/low gain switching unit of power causing the instant drop just after initial attack.
My next approach will be to replace the coupling caps for the corresponding voltage sources. For those interested it is the set of 3 caps that are glued to a set of 3 inductors right next to the transformer. If this works i'll post my results.