I have two problems with my Focus 2001 ZTS, one is that when the car is driven, I can here a thump noise. I changed both front struts and balanced the tires and the noise hasn't gone away. Second problem is that the car engine hesitates and wants to shut off unexpectedly, i do have a manual trans.

SOURCE: Tire wear

google TSB 03-13-5 (addresses concerns over excessive inner-tire wear on wheels mounted in the rear.), then contact your dealer again.

SOURCE: 2004 Ford Focus ZTS engine whine/ noise

The exhaust system on this vehicle has to be able to flex or it would crack at one of the joints, so it has hangers with rubber bushings to hold it into place and still be able to flex with the engine. Now grant it one of these bushings may have come loose or one of the hangers may have broke but I would be concerned about the thumping of the exhaust against the floor board. This could be caused by a broken motor mount letting the engine flex to much. I would suggest having someone inspect these.

SOURCE: NO heat in front of 2001 windstar van. Thumping

Blend air door may be stuck. I removed a pencil from a heater box before. It had fallen from the dash, down through the defrost vents and jamed the door.

SOURCE: a rattleing noise when hitting small bumps?

have you checked the sway bar end link bushings?