When do you feel the thumping in the clutch pedal? When the clutch is pushed to the floor, when it's engaging/disengaging, or when when its up all the way?
Have you inspected/replaced the power steering belt? If the belt is too worn (loose) it will squeal if it's not able to turn the wheels.
What is the condition of the axles?
Are there any indicator lights on (CEL)?