Thanks again everyone. I am going to raise the seat a little and see if it helps and do some shorter "Test rides" to see if I notice any difference. Than try the commute again next week. I am shooting for 4 days a week and speed is not an issue, I leave the house plenty early so I can take my time and not have to worry about being late to work.
The Plus side to commuting is my wife said I can buy a new bike if I keep up with the riding.