Unless something has changed recently, right/left alt and right/left ctrl do not work correctly in keyclone. If I remember correctly, it had trouble sending right modifiers across machines, and converts them to left ones even on the same machine.

Try switching your keymaps from right modifiers to left modifiers.

Based on what you said and examples you gave, the problem isn't in wow, so it has to be that keyclone isn't sending the correct keys. However, apart from using right modifiers, I can't see anything else wrong with your keymaps.