Cylinders

As long as you are CERTAIN that no small particles of metal have circulated with the oil to do damage elsewhere, it is OK to replace/repair just the damaged parts. You should also verify that the valve guide did not sustain damage from the broken valve stem (if I understand your description correctly the valve seat is damaged and so might be the guide).

There is no reason not to repair the damage to the head, but the piston obviously is trash. Well, maybe it's not trash and if it is merely dented, not punctured or out of round, you can probably still use the piston. When I bought my '56 Type I the seller was honest about a problem with the transaxle (he was wrong - it was just sloppy shift linkage) but I discovered that there was a hole in the top of #3 piston after driving it for a while. It did not run very well, but it ran. This is how I know about the damage from metal particles circulating with the oil. Bummer.

While the engine is out and the head is off, and especially if the case is split, would be a good time to consider whether you want to get the job done with as little cost as possible now, or to spend more and do more work to improve your chances of running the thing a long time without needing to do more work later on. If money is no object (yeah, right) the choice is easy.

Best regards,

Rob