‘04 S here. I just replaced the clutch and pressure plate, an axle, and the timing cover gaskets. I also did an oil and filter change. In order to accomplish all this I removed quite a few components from the engine compartment (via FESM) to allow access to the shift cables, steering knuckle, etc.. Once everything was back together, I started the car and came up with P1689, P1242 and P1109 OBD codes. The car has never run rougher. I’m reading that it could be a vacuum problem. Has anyone experienced this issue before and if so, how did you solve it?

 

Solution found for P1689, P1242 and P1109 OBD II codes: There are three separate vacuum lines that attach to the supercharger. One goes directly into the supercharger right above the end of the supercharger air plenum (where the green gasket is) opposite the throttle body. The line itself has a protruding circle approx. one inch from its end That line was plugged in but not fully seated down to the protruding ring. There are also two other similar vacuum lines that fit into receptacles in the middle of the supercharger air plenum. These two lines also have the protruding circles. They were plugged in when I installed the plenum but evidently worked themselves out (very hard to see from above). Repair tip: Use a pair of needle nose pliers on the tubes just above the protruding circle and without squeezing the tubes press down firmly. All three vacuum lines should be fully seated all the way to the protruding circles. My pain is your gain because my Mini started immediately after this repair and runs perfectly after this fix. I hope this helps someone in the future. Cheers.