#2 and 3 ignition leads reversed

In order to adjust my valves I had to take off the ignition coils, and in doing so noticed that the #2 and 3 leads are reversed - that is, the lead that is supposed to go to the #2 cylinder was going to the #3 and vice versa. Now the bike has been running great so I'm actually a little afraid to switch it back to what is right according to the service manual. Shouldn't something horribly wrong have happened if they are indeed reversed?

No. One coil fires plugs 1&4 and the other coils fires plugs 2&3. These bikes use the wasted spark method. So, for example, when the coil fires plugs 2&3 it fires both plugs at the same time. One cylinder will be at the top of the compression stroke and its fuel charge will ignite, the other cylinder will be at the top of its exhaust stroke and the firing of its plug will do nothing. Because they both fire at the exact same time, it doesn't matter if the #2 wire it on plug #3 and vice versa. The same applies to the coil that fires plugs 1&4. Ed

2 and 3 run off the same coil and spark at the same time ( with a wasted spark) so it won't make any difference.
Same goes for cyls 1 and 4.

Ah, nice, that explains why it's still running well. Thanks!