Thanks Doublecabin, I talked to a lady that has hiked the area and she pointed out a few flaws in my route, basically places where I'd run into cliffs. I think I have several possible options now. I'll probably skip the trail between the lakes since no one seems to know about it and its really a dead end anyway.
What I'd ideally like to do would be start in the north and hike across Eagle pass, through the corner of Yellowstone, and then more or less along the continental divide and come out at either Brooks Lake or the Five Pockets. That is IF I'm able to meet my brother up in there and arrange a shuttle. If not I'll be working out some kind of loop.
The loop will depend on YNP permits, any ongoing fires etc. but I'm pretty sure whatever I do I'll hit that section of the continental divide between Crest Mtn. and the Younts Peak area. I've also heard you can go cross country along the ridge from the Buffalo Plateau to what some people call Tri-County Lake (its not named on some maps). From there I could drop down to the Two Ocean Pass area and finish the trip on some of the more popular trails (where I'm less likely to get lost at the last minute)
I'll keep the deadfall issue in mind. I've tried not to plan any routes where I know there have been fires, I know that won't completely solve the problem but I figure it will help.