I've searched for days to find a plugin that does two things - lets me use a custom template stored in the theme directory so that it's not overwritten with updates and allows me to set a custom login page to be excluded from the maintenance mode.
This satisfies both those requirements and does it wonderfully. The first it does with a custom 503.php page (which fits in nicely with my 404 and other error pages) and a basic text box in the back end where I can write in my excluded pages. It's just perfect. And it works. Really, what more can you ask for.