There can be many causes for missing tones in a HammondOrgan.
Here's only a few hints to get you started.
If the same tone is missing on both manuals, and on all drawbars, the problem lies either in the ToneGenerator or in the wiring between the TG and the manuals.
See http://www.dairiki.org/hammond/wiring/ for a handy clickable wiring diagram which will help you find where your trouble might be.
Broken Wires
Probably the most common cause of this type of problem is a broken wire at the ToneGenerator (or possibly at the manuals.) Look at the TG and inspect the wires coming from the manual harness for breaks or bad connections. (A chart detailing the locations on the TG of the connections for the various tones can be a big help, since it will tell you exactly where to look for trouble.)
Jammed Tonewheels
If the organ has been moved without LockingDownTheToneGenerator, the TG magnet rods can get jammed into the TG to the point that they hit their tonewheel, and stop it from spinning. (If this is the case, you will be missing (some multiple of) two tones --- the tonewheels are on slip-clutches by pairs.)
Less Common Problems
TG pickup coils can open up. The wiring between the pickup coil, the filtering network and the TG terminal strip can be faulty.
Note that you can use a standard pair of stereo headphones (and a couple of nerd-clips) to check the tones at the output of the tone generator. (Just hook ground to the chassis, and tip and/or ring to the TG output.)
Causes:
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