So you still have the old car and you can try swapping some parts over. I would start with the fuel pump relay.
It would be helpful if you give more information about the rough running, is there a strong smell of petrol from the exhaust when this happens, does it idle rough but pull more smoothly, etc
'08 Chrysler 300CRD (MB OM 642 engine)
'95 E220 estate
'89 230TE (R.I.P.)