My 1998 A6, has misfired a few times in cylinders 4,5, and 6. my mechanic thinks it might be the coil. does this make sense? i don't want to drop $350 if that's not the problem.

 

most likely coil packs indeed, about $40/piece plus a little labor.
Though I don't how cylinders are aligned/numbered, but if they are all on one side, it could be coil pack amplifier. i am sure others will keep me honest on this

 

Agree.. would also look at the injector wiring and drivers.