Code 12 is nothing, that just indicates that the battery has been disconnected/reconnected in recent history.
First, you can remove your throttle body spacer. With the air-only type of throttle body used in the TJ, spacers can't/don't do a thing. Spacers only help when under carburetors and the older style TBI throttle bodies where an air-fuel mixture passes through.
So when does the slow start occur? Only after it has sat a while, like overnight?