This is the order I'd check things.
Check tires for proper inflation.
Change oil and filters (air, oil, breather, fuel, cabin) Do them all, don't be a wussy.
Wires.(Mikes right, no wires. Disregard this line)
Mass air flow sensor.
(edit: EGR Valve, then DPFE Sensor http://www.focushacks.com/mod/DPFE_S...GR_Information
Give it to the dealer and have them test it.
Start at the top ignore all the ones you've already done, and feel free to also do other peoples suggestions.