Tried out the test that you mentioned for continuity with the footswitch disconnected. Between pin 9 and 2,3,4 they all showed about 6 ohms. But when I tested it between 9 and 1, it did go to 0. Also like you mentioned, I turned the amp on with the footswitch disconnected but the switch in the Ft. Sw. position, and yep, it stayed in the Rhy 1 channel.
As far as the test that Mesa suggested, it powered up, but still Rhy 1 light stayed on and would not switch to any other channel. Again, Loop and EQ would light up when pushed. The readings on pin 1 and pin 2 were about .5 volts, constant even if I pushed the individual channel buttons.
For the heck of it, I checked my FU-2A footswitch and here's what I got...
________Pin 1_____Pin2
Rhy1____0v________0v
Rhy2___3.5v_______0v
Ld1_____0v_______3.5v
Ld2____3.5v______3.5v
The 3.5 is where they were expecting 5v and on Ld1 Pin2 their diagram showed .5 volts, but either way you look at it, there's voltage where there should be, and not where there shouldn't be. From what I can see, this confirms that there is a problem with my FU-3 footswitch, probably the IC like you suspected, and also most likely something in the Mark IV switch since the FU-2A is working correctly, do you agree? I will probably order the IC switch and see if I'm able to change that out if you think that's the problem, or do you think there's more troubleshooting needed on the footswitch? I'll get to the Mark IV switch later.
Thanks!