Clunking Noise??? What is it??

I have a manual 94 SL with 108K. Did the 60k service at about 69k. Car has never been driven hard since I have owned it since 22k. Oil is changed regularly and closely monitered. No excessive oil usage. Oil pressure appears fine.

The car made a clunking sound on startup yesterday. NOT lifter tick. Much louder. In addition, it ran really rough like it was not firing on all cylinders. After a 15 or 20 seconds it started smoothing out and the clunking sound started disappearing.

My first question is, would missing on a cylinder or two cause this clunking sound? Secondly, what is the most likely problem?

Thanks,
Dave in NC