The multiple changes in chamber volume slow the exhaust gas velocities and cause you to lose exhaust flow and therefore power. Your best option is to replace/gut the precats, and empty the debris out of the main cat, just pour it into a bucket. If the symptoms persist, you'll need to have your main cat replaced.
I don't know what your mechanical capabilities are, so if the Mystery Mod how to is not to your liking, you can get a set of gutted precats from buckshotmotorsports.com for under $100 (after your core return) and have those installed. Easy and comparatively cheap.
