I have also just purchased a 1998 Suzuki Intruder 1500 with 18000 miles in 12/2004. It has cobra drag pipes and custom paint. Otherwise it is stock. It has not had a major tune up since it was new; therefore, I took it to a local dealer for a front to rear service. They performed a 18000 service which included syncronizing the carbs(verifying that they were "jetted" for the Cobra pipes), adjusting the decompression cable, and a complete tune up. Also they had to replace the rectifier/stator/battery too. After a $850.00 service the bike runs as new and the backfiring is still there but a lot less noticible (I was told that was inherent of the Cobra drag pipes).
I know that this may be old news now; but if not, I hope that this will help with your bike.