The previous replies are all on the mark. I've never done it by the square foot, but by the outlet. Categorize the outlets and price them. A bedroom outlet within 10 feet of another bedroom outlet will be less than the switch outlet in a four-way switched light from the entry to the second floor hallway. I prefer time and material, but the price-for-the-worst (and let the easy ones create profit) method is fine also.
Sometimes the slow jobs are good if the customer will let you schedule your own time. That way you can use it as a fill-in job. There's nothing wrong with an $18-19,000 fill-in job! I'd ask for a few extra payments along the way so I wouldn't be paying for materials out-of-pocket for three or four months.
Dave
