N,
That is a concerning problem. If i understand correctly, you replaced the rod. I was going to suggest a broken head stay but it you checked the top end then you have already had that off and would have noticed. The only thing I can suggest is that the crank halves may have twisted a bit on the rod pin (new rod?) putting the crank halves way out of balance. I can't think of anything else. My K5 hardly vibrates at all. I would wait for a few more ideas from stewart and the other engine guys before you disassemble. You might be able to verify this with a dial indicator on the crank with just the top end off to see if each side is the same. Hope this helps. Cam.