For two months, your best bet is to find a local who is willing to store your car for you. You might try sending an email out to the pct-l to see if someone can help. I’ve had good luck with the list in the past. You can sign up for the list at http://www.backcountry.net
I would say that if you want to start at Yosemite, it will be more convenient to fly in to Reno and then catch a CREST bus south to either Lee Vining or Mammoth. From Lee Vining it is an easy hitch to Tuolumne. If you go to Mammoth, you can ride a shuttle bus up to Reds Meadow, through which the PCT runs.
If you have a PCT permit, you should be okay. The permit should have your starting location and be issued with the authority of the land management agency where you begin.
Suge