By September 13 there is a good chance that Yellowstone will have had at least one hard freeze. Most of your smaller birds will be out of the park and at lower elevations. You may see smaller guys around thermal features and along the warmer firehole river.

I would strongly recommend a side trip to the Red Rocks bird refuges between I-15 and Henry's lake. Good place for hawks, eagles, migrating ducks, and one of the few places where there is a resident population of trumpeter swans. You should be able to learn to identify swans by vocalization. Follow the dirt road to Henry's lake for a 2nd chance at Swans.

Terry McEneaney, is the park ornithologist and has written a couple of birding books. He is based at Mammoth but isn't much of a sharer but may post sitings at the Mammoth visitor center. Stop and scope swan lake just south of golden gate.

http://www.nps.gov/yell/naturescience/birds.htm

There may or may not still be Sandhill cranes along The Madison River, about Hayden valley or the Lamar Valley. Golden eagles should be about the lower Lamar around Slough creek where there is a summer nest. Mt Goat are regularly seen on Baronet peak on the upper Lamar, bring a high power scope. Fall Grizzly wolves can be seen on the Lamar, Hayden peak and Hayden valley. Falcons may be still about Yellowstone canyon between Tower Junction and the Tower falls turnoff. Bighorn sheep and grouse along the road to Hayden peak.

Follow the Yellowstone river South to the LeHardy rapids for Harliquin ducks. The Fishing bridge area east to steamboat for local ducks and osprey. The fishing bridge ranger station does maintain a birding log.

Plan to camp at least one cold night at Norris campground and listen to the elk in rut in the meadows just off of the campground. Buffalo will be everywhere. On the way back home stop in Bozeman and follow directions from the Montana Audubon society.

Go north from Missoula to St Ignatius for a number of small local refuges and for the national bison range, for a wide range of native birds, still around at this lower elevation.

The park will be closing in bits and pieces. Be prepared for snow, and to take advantage of gas and food when it is available. Late night and early morning will still be the best times for critters, but most animals will be down from the high country and active for the mating seasons.