Ah, I think I understand the purpose of the warning in the shop manual. It's a safety issue.
If you think about it, turning the flywheel clockwise from the alternator (right) side is actually the same direction that starts the engine, i.e. counterclockwise as viewed from the pedal starter (left) side of the bike.
Although it is not stated, there may be a (remote?) possibility that rotating the flywheel clockwise (facing the alternator (right) side of the bike) might result in an unintended starting of the engine, which could be dangerous.
i think the problems in the electrical system are unrelated to the turning of the flywheel. Perhaps the previous owner connected the battery backwards, and possibly started the engine too.