Instead of the Northern Loop, try the eastern half of the Northern Traverse: Chief Mtn Customs trailhead through Stoney Indian Pass, ending up at Goat Haunt. One of the logistically easier through-hikes to set up in the northern part of the park. I just did it as a 3 day-2 nighter 8/25-8/27; great time, even better views.
On the morning of the 1st day, drive your car up to Waterton, leave it at Tamarack Outfitters, and take their Chief Mtn Shuttle (make sure to reserve a space by telephone beforehand):
http://www.hikewaterton.com/shuttles/
You'll end up at the Chief Mtn Customs trailhead a little after 3pm, enjoy your hike at your own leisurely pace, take the boat ride out of Goat Haunt the last day (
http://www.watertoncruise.com/goat-haunt.php#2), and your car will be waiting for you back at Waterton.
I was a little too ambitious the 1st day and set my campground at Glenns Lake Foot, thinking that 10 miles is nothing. I forgot to take into account that because of the shuttle schedule I'd be starting out at 3pm, so I was rolling into camp slightly before 8pm. That left me only 1hr to set up the campsite, cook dinner, and get ready for sleep before it got dark. Probably a less hectic plan would have been to set the campground at Cosley Lake for the 1st night.