re: Glacier NP- lottery system/general questions

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What's the weather typically like at that time?

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Depends greatly on what elevation you are at. Whitefish might have highs in the 60's that time of year while Logan Pass might be highs in the 40's.

You should be fine late September, chilly but not downright cold unless at higher elevations that get real windy (like Logan Pass).

Might be too cold at night for the Under Canvas thing, I've heard of them but have not stayed there. I've had good luck with a couple of AirBnb's in the Coram area that are just outside the western edge of the park....

West Glacier AirBNB's

We stayed at the cabin below this past summer and had a blast:

LINK

Stayed here a few years ago and liked this place as well:

LINK

AirBNB's on the eastern side of the park, we stayed at a hotel in Browning next to a casino on the Blackfeet reservation, which worked fine.
East Glacier AirBnb's

If you had a full week to do a trip (assuming 5 days actual with 2 days flying in/out), I'd do:

Day 1: Polebridge/Bowman Lake
Day 2: Going to the Sun Road (Lake McDonald, do Highline trail hike, maybe not the whole thing but the 2-3 miles from Logan Pass. Also do Trail of the Cedars hike and stop at most of the major stops on the road for sightseeing).
Day 3: Two Medicine area on Eastern side of park (they have boat rides on the lake here that are pretty cool).
Day 4: Many Glacier Area (Apikuni Falls/Iceberg Lake hikes). This is my favorite part of the park but has had terrible construction the past year or two resulting in 2-3 hour delays to get in there. Hoping that wouldn't be the case for your trip.
Day 5: Drive back to western side of park (using the Going to the Sun Road to see all those views again) and do the touristy/fine dining things in Whitefish that afternoon/evening.

So you'd stay at an AirBnb on the western side for nights 1-2, AirBnb on eastern side for nights 3-5, and then a hotel in Whitefish for night 6 before flying out the next morning.