Thanks for all the feedback. It's well enough to get me going - I'll make a start this week.
The majority of decent alarms have an ARM signal, so there's no reason why it can't be attached to any make. You'd need to trace it though - some are pos but most are neg. It just goes high or low when the alarm is set.
I was thinking about using the indicator flasher as the arm, but it would need more circuitry as the indicators flash twice (or more depending how you are arming it), so it would receive multiple signals. The other concern using that method is if the signal gets 'back fed' (i.e. the dioide is in the alarm itself where they usually are) then the signal would trigger the mirrors when you indicate or have your hazards on and the alarm set. We could put a diode in ourselves but I don't want to cut into the line, simply attach to it (just to keep connections to the car itself to a minimum). I'll check this line out though.
As for total closure, I'll need to look more into this. The passenger and rear windows use current sensing on the power windows, not a sensor for when they are fully closed. (Try and close all the windows when they are already closed - you'll see your dash lights dim dramatically - same thing would happen if closure power is applied by an external circuit). As the system won't know if the windows are closed or not, it would still send the power to them for a pre-determined time - I'll need to spend some time on it but I'm just a bit concened on the current drain. I could build a secondary current sensor in myself that would stop the power if the current pulled was greater than a set amount. This would also take care of the safety issue but I would be worried that if there was something that caused any friction and the windows pulled more current than normal, then they wouldn't close as the power would shut off to them and leave the windows open.
For now, I'm going to keep it simple and cost effective. I'll just do the mirrors and look into the total closure when that's complete. It should be a quite easy to add on as it will have most of the signalling and control circuitry already in place.