If you follow the suggestions about having NOTHING in sight (maps, papers, box of tissues, etc) inside your car, I seriously doubt that your car will have any problem. There are a lot of cars there and the only reason a bear will attempt to go in is if it can see something worthwhile for the effort. They are not stealing cars, they after food they can see. They are not dumb nor are they mind readers. If they can't see it or smell it they won't waste the time but pass you for the next who may not be as careful as you. They don't reserve parking stalls for dinner, so broken glass is just a sign of a careless car owner not smart bears. Hope you don't smell up the mountains with air freshener either
I'd not leave any food in the car. Just plan on buying more at Lone Pine when you return. Canned food/liquids are fine so long as they are not visible or opened. The wrapper they came in NOR the bag from the store that packed them must not be visible. This includes empty beverage cans. A paper bag full of dirty clothes on the floor of the back seat looks the same as a bag with a Christmas turkey and all the trimmings to a bear.
Could be the cleanest the inside of your car has been in awhile. Take advantage of the occasion to tidy up after the long drive up there.
If bears were the threat most people have come to think they are, you can bet the rangers would not let people traipse around up there let alone park. Bears are easy to control and figure out so long as there is no food involved or young cubs.
They will not hijack you on the trail or take over while you are eating. It is prudent, if they start walking toward your camp, to secure any food in a canister and aggressively defend your territory. This includes making a lot of noise (to alert others in the area) and holding your ground...up to a point. If they keep coming just keep making it noisy for them and step aside. They don't want you -- just the stuff you brought to eat.
Don't let the bears ruin a good trip for you or cause you to think you will have to park in Lone Pine. There is a better chance that you will not see, hear, or smell one while you are there. If you do, think of it as a photo opportunity...from a distance.
Raccoons are a lot bigger menace where they occur. Usually a lot more of them and they are more brazen. Not a lot of media interest, though.
If you have extra time on your permit I'd spend it after you get back from Whitney rather than on the way in. If it is your goal to get to the top, then do it. Then take time at a nice restaurant in maybe Bishop or Mammoth (St Mary Lake has a lodge with wonderful meals). If you are going to be there before your permit, I'd take in some of the fun stuff in the area that is lower down. OR take a short hike uphill from perhaps Onion Valley parking lot west of Independence. There are some early lakes to take a nice day hike and lunch to (with a nice book and some skeeter repellent) or if you are ambitious make a run for Kearsarge Pass or just below it. But give yourself a rest period before hitting the trail up from the Portal. Having time between 6,000 and 8'000 is still acclimating if you are up from San Diego. You don't have to stay at the Portal, Onion Valley, or Horseshoe Meadows to get the advantage of altitude.
But if you must
http://www.mtwhitneyshuttle.com/ about $100 if that will give you better peace of mind over the few days you should be enjoying where you are and what is included in the price of the effort to get up there.
And you can probably hitchhike up there and back a lot cheaper
). 
