I wouldn't lap anything unnecessarily, and even then, if it's not done properly the new rifle could be degraded.
What's the problem with the bullets, their composition? Does Savage recommend using only bullets constructed of certain materials when using smokeless powder?
There's forums specializing in the Savage muzzle loader to get expert & experienced advice:
http://www.modernmuzzleloader.com/phpBB/ (Has a Savage dedicated forum section)
http://www.savageshooters.com/ (click on "forum" at the top of the page)
Good luck and enjoy your Savage!