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You haven't provided a model number, but based on Yamaha Organs in general, The first thing is to check the power supply voltages, especially the plus and minus used by analog sections. You should find a +/- 12 volt and/or +/- 15 volt supplies. These power the analog sections and if one is missing, the symptoms would be as described. This would be the case with the FS30 and similar models. If yours is different, please let me know the model and we can go from there.
If you have it open for inspection, check all the capacitors on the power supply - just a visual inspection. That may reveal problems with bulging or leaking capacitors, which are an easy and inexpensive fix.