i have a 99s3, i had some of the same problems. i would replace all the intake and exhaust gaskets, make sure everything is tight and no leaks. use the ecm spy and reset the tps and afv. this helped with my bike, i have had to tune a little bit to get the popping out.
i have eproms for 99x1 stock and my s3 race eprom, i will share if you need. you have to make sure you have no intake or exhaust leaks before you try to do any tuning or tps resets!!!