Yes, you can pick up a Yosemite wilderness permit for which you have reservation at any Yosemite permit issuing station. There are permit issuing stations at TM, YV, Big Oak Flat (the hwy 120 west side entrance), Wawona, and Hetch Hetcy. See
http://www.nps.gov/yose/planyourvisit/trailheads.htm for the listing of THs and stations. I almost always pick mine up at Big Oak Flat. I recall them being open ~8:00-4:30 or thereabouts, but you may want to call and check the hours. Be sure to call 1-2 days ahead if you'll be arriving after 10 a.m. on the 1st day of your reservation.
There is some Meadow Fire smoke info at
http://californiasmokeinfo.blogspot.com/2014/09/meadow-fire-september-14-2014-meadow.html .
