Like everything back then, the MIDI part of the manual is.. well, looks like it was written by someone who didn't know what they were writing about - which is probably true. Sad thing is, it hasn't gotten much better with modern MIDI gear.
Have you tried the PC messages? At the top of Appendix C it says:
Program change:This is a regular PC (program change) message. The FCB takes care of the channel (and if the SGX is set to OMNI, channel won't matter). So a PC 00-127 will recall the first 128 (of 200) presets from the SGX. The number you see on the SGX will be one more than the number you send via MIDI to recall it. So if you want to recall preset 94, you use PC 93.
x = channel number 0h to Fh for channels 1 to 16
dd = program number 0h to 7Fh or 0 to 127
For CC messages, did you set Performance MIDI mode for the preset? It looks like you need to turn that on (page 49) for every preset you want to control with the two FCB pedals. Jack has it right, when you turn Performance MIDI on you have the option to change the CC number from 04 (the default) to whatever you'd like. The chart also says CC's are used to turn effects on and off. The chart at the bottom of page 54 lists these:
EXCITER 70So sending a CC 78 with a value of 0 would turn off the Flanger/Chorus. And a CC 78 with a value of 127 would turn it on. The 0 and 127 are standard for off/on, but some devices reverse them, so swap them if you need to.
EXPANDER/NOISE GATE 74
PITCH TRANSPOSER 77
SPECIAL EFFECTS 79
Another thing to try would be connecting it to a PC with a MIDI monitor like MIDI-OX. The manual mentions it has a MIDI monitor built in, but I didn't read it closely. Start up the monitor and move the pedals, and you should know which CC numbers to use.
As far as SYSEX messages, there are two reasons to ignore them. One, the manual is a bit cryptic about everything except switching OMNI mode. The other reason is that the FCB can't send SYSEX messages.
Hope this helps.