You are going to have an amazing trip!
I did the JMT in 2011 in the same time frame, late August to Sept over 15 days, one of those being a zero day at VVR. (Great place, highly recommend it....they love thru hikers, unlike MTR).
Anyway, I wore REI convertible pants and had problems with the excess fold of cloth on the inside of the pants that covers the zipper and prevents it from contacting my skin.
It was rubbing my inner thigh raw after 120 miles or so.
To the point where I needed to put tape on my inner thigh to protect it.
After that trip, one of my first purchases was REI pants that were non convertible.
Plus the reality was that I never converted them to shorts for purposes of sun protection and I simply am not a shorts person.
In hind sight, I realize if I had some zinc oxide to put on the areas that were chaffing, I would have been much better off.
I now carry a small jar of zinc oxide in my med kit.
Anyway, hope this helps.
Be safe and take lots of photos on your adventure.