You'll enjoy the trip no matter where you go. What entry point are you closest to? Elkhart, Green river lakes, or big sandy? I'm pretty sure fishing will be good no matter where you end up going. The temperatures are cooling off and the fish are hungry for the winter. The weather this time of year stays unpredictable but you'll have rain gear so you wont have to worry. Temps will be cold at night so pack accordingly.
Suggestions: The cirque of the towers is always a wonderful and iconic view of the winds. From elkhart going up to the titcomb basin is, IMO, the best view of the winds. Fremonte Peak from island lake is my favorite spot in the winds. I've never been to the northern region but, like the rest of the Winds, I'm sure you won't be disappointed. My vote - Elkhart to Island lake.
Have fun, and if you have time write a TR.
Salud!