I fly from San Francisco and find the best prices 8 to 9 weeks prior to departure. I know the urge is to book the flights at the same time you make WDW reservations, but patients can save you some money. You will typically find lower prices for Tue, Wed, Sat flights and higher prices on Fri, Sun.
For example, in Dec/Jan Tuesday flights 10 and 11 weeks out were running around $477 to $467. I booked in week 9 for $320.
As for the Disney Express, you can call to update your flight information any time prior to 45 days of arrival.