There isn't a schematic available, so this is just guess work:
On the older 3 Channels, the ftsw and the fx loop were supplied 15 volts for switching. Your amp seems to be using 12 volts. Since your loop is series, the circuit is different from the old one. However, Mesa often uses jfets for switching. On the old schematic, two resistors, a diode, and the 15 v supply were used for a switch and to power the ftsw.
Your amp seems to use those resistors, diodes, and the jfet along with the relay for the loop and part of it runs to the rotary knob and DIN (probably as power). If something failed, it could be pulling power to ground and reducing the voltages. Since your ftsw doesn't work, the problem is very likely on that daughter board right around where the resistors are, or up/down the track from them.
The cathode of one of those diodes is going to point right to the pin of the DIN that needs power.