Doing trail work, I am often a sitting target (literally) for mosquitoes in the Sierra. They LOVE me, and they drive me crazy. So, although I'm trying to eliminate chemicals from my life, two summers ago I finally broke down and decided to treat my clothing with Permethrin. Bought two bottles; followed the directions to the T; and treated pretty much everything but base layers, down, and rain gear. I did not notice any difference in the mosquitoes' interest in me or the number of bites I got.
I'm not sure about ExOffico's anti-bug clothing, but a friend of mine thinks her ExOfficio hat keeps the skeeters away from her head. As far as more natural products go, I now use Herbal Armor™ Insect Repellent; it works surprisingly well! Cutter's "natural" bug spray products seem to work okay too. Of course, if you're going as light as possible, those options are out. I'm doing the JMT in a couple of weeks and will bring a little DEET. I think you'll be okay in your regular convert pants. The bugs will probably be more interested in your feet/ankles, shoulders, head, and hands than your legs anyway.
For the morning and evenings, a head net may be the ticket to maintaining your sanity. Unless I'm super early or late in the season, I wouldn't backpack in the Sierra without one!
Have a great trip!