You mentioned vibration and someone else mentioned flex-plate. Put 2+2 together and I would guess a rod should not cause vibration. And when you say rod, do you mean rod bearing?? I have changed these out before by simply dropping the pan. I don't believe a fresh rebuild , broken in with care, should have a bearing prob...... I just don't buy it!
Keep investigating and go buy a stethy csope to listen in and you will isolate a whole bunch of things and rule out a whol;e bunch more.
