I applaud the ingenuity and I'm a huge fan of using stuff I have on hand! If it works it works! In the future if you want to get a kit with a big K&N style filter they sell the kits on ebay for 29 bucks with free shipping.
My theory is that the header caused a lean condition, assuming you didn't rejet since you didn't mention doing so. That tiny filter is more restrictive than the stock filter thus creating more vacuum drawing more fuel, resulting in richer mixture.