the secondary intake system has nothing to do with the misfire. you have two seperate problems there billycuth.
Your secondary air flow too low code is telling you that your air pump, located on the rear drivers side of the engine compartment is either dead or dying. What I would do is check ALL vacuum lines, especially the ones connected to the no-return valve and the ones under the intake manifold. here is a link that tells you some symptoms of a failing air pump and how to replace one, unfortunately for you (and me
), it is very expensive. On the bright side however the only problem it posts is that you might not pass emisions until it gets fixed. The reason for that is because the purpose of the air pump is to pump air (who would have thought) into the exhaust manifolds to aid in the catalyzation process, thus giving you cleaner exhaust.