I researched a similar trip last year and discussed the permit issue with the Wilderness Permit office. (different start point but similar climb of Whitney without exiting at Whitney Portal).
From Kennedy Meadows PCT to JMT Junction, climb Whitney & return to junction, take PCT or JMT to Yosemite (Tuolumne), then JMT to Yosemite Valley.
You start in the Sierra South Wilderness, part of Inyo National Forest. (Trail Code S 65) You will need a wilderness permit, but there is no quota for that trailhead. The permit will cover you all the way to trip end at Yosemite Valley as long as your dates and route are generally correct.
South Sierra Wilderness (Trail code begins with S)
Permits are required year round for overnight trips.
Trails are not limited by quota
A Whitney exit quota exists if you are starting from an Inyo NF trailhead and passing through the Inyo NF "Whitney Zone". Your route does not pass through this zone because the JMT from Crabtree to Whitney summit is entirely within Sequoia National Park.
Whitney Zone map: http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb5130080.pdf
Also note that the Whitney Zone and JMT from Crabtree JCT to the summit is a "pack out your solid human excrement" zone. This applies only to those exiting at Whitney Portal (as carrying your &hit for another week would probably be a violation of EPA rules.) Still, try not to leave any deposits above treeline.
Call the Wilderness Permit Office in Bishop to find out how to pick up your permit- I don't know if there's a ranger or self-issue station at Kennedy Meadows.
Wilderness information phone line is open 8:00 am to 4:30 pm
During the summer season open every day from May 15 to Oct. 15.
During the winter season (Oct. 16 to May 14) closed on weekends and holidays.
Phone: (760) 873-2483
-Horseshoe Meadow is very close to PCT- in fact if you go out over Trail Pass and back in over New Army Pass you do a little more climbing but only a couple more miles. No store, phone, or scheduled transport to Lone Pine. Also it's only 50 miles from the start.
-Whitney Portal- Need the permit plus it means carrying your whole kit to 14,000' and down/back up from 8600'.
-Kearsarge Pass/Onion Valley- About mile 115 including Whitney sidetrip. Have to hitch to town and pick up a package at PO, or hitch to Lone Pine or Bishop for decent grocery selection.
Then of course Muir Trail Ranch or Vermillion Valley Resort, Red's Meadow, and Tuolumne Meadows.