A few possible causes. (1) check coil pack. (2) check fuel pump. (3) Check idle on injector assembly.
Fords are notorious for coil pack problems, about £60 for a new one, if fitted yourself.
Fuel pump may be starting to give out, try replacing it.
Idle may need adjusting maybe due to stretched throttle cable. there is also a possibility that if you have run your fuel extremely low, the pump may have sucked some debri up (ie rust) from the bottom of the fuel tank and may now be clogging the injectors.
Matt, July 2009