if you start tuneing/modding a motor,you need to keep/make bench marks,your bis may have an ailment caused by ragging it after fitting the exhaust,sometimes you need ''regression therapy''.....that means,put the old exhaust on/remove last mod and see whats what.
but,from what your describing id say its nowt to do with your new pipe...if you have been hooning around the carb might be full of stirred up pooe etc.......lots of things can cause the probs you dscribe.............. :cool:
think about the last time your car ran well,then ponder on what you've done since...............dont poke anything till you've thought it thro.......otherwise you'll just muddy the waters further