another forum thread suggests these codes indicate insufficient fuel into the cylinder. The AFR is calculated based on the MAF reading, if you've got a vacuum leak between TB and intake, then you'll be putting extra air into the engine that isn't accounted for. this would cause insufficient fuel for this volume of air and then cause misfire and engine codes. Also makes sense that it idles rough since vacuum will be most pronounced at idle when the butterfly is mostly closed. So i'd say definitely a vacuum leak where you reassembled, you seem to be on the right track.