Halloo?
Fall is fall is fall - when.
September is nice. October is very tricky.
Plus the days get quite short & cold at the start.
You are looking at 800+ miles if you follow the TransAm route -
http://www.adventurecycling.org/routes/transamerica.cfm
From Missoula to Walden - then down Poudre Canyon to Ft. Collins.
You'd be lucky to do this section in two weeks.
Personally, US 89 from Glacier to Yellowstone is one of the nicest rides in the West.
But there is no way you have time to do this - plus make it back in two weeks.
Remember the old adage - less is more.
(Also - I think Going to the Sun Road will be closed after Labor Day for construction.)