If the misfire only happens at high rpm it could be something in the valve train, bad valve guides, slightly bent valve or maybe even weak valve springs which maybe fits at least a little bit into the overheating. I would concentrate on trying to get it running properly, and without codes without revving the crap out of it for the time being. If you haven't already, you could try disconnecting and reconnecting the connectors on the DME, trans controller and ABS (disconnect the battery) a few times to help eliminate oxidized connections.

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1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)