When running open headers, oxygen from the outside can make it to the O2 sensors and throw off the readings. That is probably what made it run funny on you. I am sure that all will be well now that you have you exhaust taken care of.

Its been right at a year since you installed your Whipple, hasn't it? Thats quite a change your truck has gone through in the last year. Its too bad this stuff is so expensive, but you only live once and it sure is fun.