RFE65 trans ? and how long was it down ? My brother works for a fleet maintenance company , their main trucks are rams, Talked to him last night, he's never had one throw a misfire code, but he's had a few run like you are describing, but only RFE65 trans , he said he would do a trans relearn , and tb relearn.
As for leaving the MDS plugs attached to the harness, I don't see why that would only affect #6 , but at this point unplug them and see what happens.