oliver, i am planning a similar trip for august this year.
i have a few different observations/different goals than you - thought i would share.
we are doing glacier becuase we have family nearby, and have tacked on tetons/yellowstone.
we fly into JAC. 2 nts. there. we want to cross the border into Idaho just to say we did it, see a few things in Jackson, wife so some shopping. Will take a ski lift to the top just for the view; kids may take the summer toboggan down, etc.
we decided to do this relatively late so we are taking lodgings that are available. I'm told the view from the jackson lake lodge is unbeatable and is about half the price of jenny lake lodgings. its also a bit more centrally located.
if you are going to yellowstone, there are accomodations in between tetons and yellowstone on what used to be the rockeffeler property. i forget the name. some of them are rustic/bare minimum, but to me the attraction is that you base yourself a bit further north with each lodging change.
i can't add much more. at the risk of stating the obvious, Old Faithful Inn is the most difficult property to get a reservation for.
we are planning to take the bear tooth highway out of the park which takes you NE and a bit and out of the way from Glacier, but apparrently worth it, and then an all day drive to glacier. the moon guide gives a couple of alternatives. We plan to drive all around Glacier and go to Waterton, so we'll probably take the most direct way to Flathead, with the caveat that we'll drive around the more scenic eastern shore of flathead lake on our way to Glacier. There is a post somewhere on flyertalk with the directions.
we'll probably buy the annual pass for $80 but i have read that a weekly pass is only $25.
One of the things we want to do is whitewater rafting. I get the sense that the rafting is better near glacier than around yellowstone.
i mentioned on the other thread that i like the Moon series of guide books.
we are renting a car in JAC one way and returning at FCA. paying about 300/week for the car this way, but its cheaper than flying between JAC and FCA.
since you seem to have some flexibility, i think the earlier you go in the season, the rivers/waterfalls may have more flow, and the wildflowers may be more abundant, but you may have more concerns about snow and adverse weather. I think this applies more to Glacier than to Yellowstone. If i had more flexibility, i might do the week after labor day just to avoid some of the crowds, although you are bumping into colder weather and more precip.