Have you tried to see if its running lean/rich? Maybe there is something wrong with the ecu. Did you reset it? (by pulling the fuse for about 15/20 mins or pulling the terminals on the battery for the same lenght of time)

1996 Mondeo 24v 4-door twin janspeed stainless pipe cat by-pass Phase 2 RS bodykit 16" cosworth alloys K&N RU3530 SVT TB/UIM/LIM poly bushings konis/bat springs/bar Pioneer MSDS Indiglos P&P heads 2005 Mondeo Zetec Tdci