I have a 2006 Pontiac GTO. Its has a 6.0 LS2 v8. I have a K&N cold air intake, magnaflow exhaust, no catilitic converters, and still has the OEM computer settings. The car tries to stall out and sometimes shuts off completly when you roll the windows down or if the A\C is on full and you stop at a read light. I just replaced the battery and the Alternator checked out fine. I cleaned the MAF sensor and this seem to help for about a few days but then it started again.
Unless you have modified your computer to compensate for removing the O2 sensors and having the K&N filter on it that may be your problem. Todays converters don't block exaust like the ones years ago. You might try cleaning your throttle plate with choke cleaner as the K&N if you oil it up to much will make your plate sticky and not work right. Make sure to clean it on both sides. Make sure your battery cables are clean.