This sounds like the alternator isn't putting out a charge until the "clunk" happens. My thoughts are:
1. loose v-belt. Does the belt squeak loudly when you first start up? Check to see that it is tensioned properly.

2. possibly the rubber damper layer in the crank pulley is loose. Mark the pulley with a chalk line across the face of the pulley from center to the edge. Start the car then turn off the engine to see if the chalk line has been displaced showing one part of the pulley has shifted. If so, replace the pulley.

3. The voltage regulator in the alternator may have worn brushes which are not making good contact with the slip rings in the alternator. Pull the regulator and measure the length of the two carbon brushes. If they are 3-5 mm, replace the regulator.

That's all I can think of for now, good luck to you!