Hoping the experts here can help me out. I have a 2005 Mini S with the dealer installed JCW package. Drive train is all stock. A few months back, it shuddered when starting from a stop light shortly after leaving my home, and would not go above 2000 RPM. I hobbled the few blocks home and pulled the codes. It reported P1688. I hate working in the garage in the winter, so I let it sit and drove my old Bronco instead. This past weekend I finally went in to take a look. I installed a Madness Motorworks JCW Intake High Flow Air Filter Replacement which I had previously purchased. I also think that one of the fittings on the vacuum line which goes to the air filter flapper was disconnected. Otherwise I didn't see anything obviously wrong.

The intake air filter had not been changed in years - perhaps it was the original. It was in bad shape, so I believe the engine is receiving a lot more air than it was. It is difficult to quantify, but I think the overall performance now is improved with the new filter rather than the old clogged filter. I also did the tweak to keep the flapper for cowl air open all the time, rather than only opening at 4500 RPM.

After doing this, the Mini runs great at speed, and I haven't had any codes. But it has a terrible idle. It pulses between 1100 RPM and 1400 RPM. Never goes any lower. Very occasionally will go to 2000 RPM at idle. Period of pulsing is about 2 seconds. I haven't been able to figure this out. Any ideas?

A couple extra notes. Sitting that long caused the battery to drain completely. It was brand new. (Just replaced the factory battery - over 12 years! I was amazed.) So all electronics were reset.

Additionally, it seems that something is getting overheated. The oil temperature gauge and the water temperature gauge report exactly what I expect, but after a drive I can smell something too hot. And opening the hood it seems like the temperatures are higher than previously, but that is an unreliable test. I think it smells a bit sweet like coolant, and there are previous stains indicating coolant leak, but I've never been able to find them. A visit to the Mini dealer last fall for recall work plus a bunch of maintenance reported no coolant issues.

And finally, when shutting off the engine it shudders, like an old car dieseling. Takes maybe a second or two extra before everything stops.

I appreciate any help, or suggestions on what to try or look for.

Jim