Thanks for the great suggestions, guys.
I've now eliminated the door switch possibility; the dome lights operate properly with door open/close and I cannot operate the windows with the door open. I also pulled the connector to the Viper and rechecked the current draw; still the same 680 milliamps.
I guess I'll start pulling relays next. I think I'm done for today at least - tired of messing with it with nothing to show.
