Well its fixed after $40.00 and 4 hours of driving. Went to the dealer and they made me do the following after setting the flags.

1. Start car and idle for 1 min
2. Drive for 3:10 at 2000 rpm
3. Stop and rev engine at 4000 rpm's for 90 seconds
4. Idle for 90 seconds
5. Drive at 2000 rpm's for 5 min - you must get up to at least 40 mph but not over 60 mph.
6. Your first trip is now set- Turn off car
7. Repeat the proccess for your second trip.

It worked great. From now on I will leave the battery hooked up and give it a charge once a month.

Thanks for the help guys.