1. I want to override the self update server location from the command line like I currently do for the application update using server/updatepath, but I don't see any command line options that cover it. Is there a command line option? If there isn't one could you add it?
You can use updatepath & urlargs.
2. What happens if wyUpdate.exe tries to get its self update wys file from the server but gets a 404 or some other error? Will it still function correctly?
It depends. If the new wyUpdate version is required to install the update, then wyUpdate will show an error if it can't self-update. If wyUpdate doesn't *require* a self-update to continue with the main update then it won't complain if there's an error.