Current wisdom is to leave the BCS plugged into the factory electrical harness. Some say that it's best to plug the vacuum ports(nipples), as well. Although I haven't found that the ports actually need to be pugged. But, be sure to reconnect it to the electrical harness.

 

[QUOTE=epson1;6334379]I thought you have EMS... EMS won't throw check engine lights[/QUOTE

Yes I do and only had that for about 3K miles. Had MBC since I got the car 20K ago.