How can I program in Yamaha MX88 the FC7 pedal in mod wheel, breath, harmonic etc.

I don’t understand the question? Sorry. What do you want to accomplish?

I want to program on my MX88 theFC7 pedal from Foot Controller jack not to increase/decrease volume (implicit, from factory), but to change to an effect (for example in mod wheel) when I push the pedal. I think the settings is in FC1, but I'm not sure I tried, no result) and I don't know if it is possible and how to do. I saw under FC1 settings a lot of possibilities: mod wheel, harmonic, volume, pan, etc. and I want to try these effects. Thanks for patience.

To change what a Controller does, you must edit the Voice. This is different from editing the Performance.

See the Reference Manual section on “Voice Edit” pages 50 thru 53 — these parameters must then be Stored in one of the 128 User Voice locations. Then you can place that edited User Voice in a Part of your Performance.

You must create your own Voice in order to change how a Controller works. Simply changing the FC1 to send cc1 Mod Wheel will do nothing to the sound (as you noticed) — what that does is simply allow the Foot pedal to SEND cc1 Out via MIDI. If you were setup to record to an external sequencer or DAW, that cc1 would be recorded, then sent back to the MX and behave as a Mod Wheel.

But the MX does not address itself with MIDI messages. This is why you must edit the Voice, the MX’s own controllers address MX parameters, directly. What you changed in the Performance Edit is what cc message it generates when moved.

Inside the Voice Edit is where you can decide what moving that controller does internally.
The MW does not have any particular thing that it does... in one Voice it might do Pitch Modulation Depth (vibrato), in an organ Voice it might be set to change the Rotary Speaker from Chorale (slow) to Tremolo (fast). This is all programmed at the VOICE EDIT level of the architecture.