You didn't give us much to go on, but there again since you bought it used you may not know the history of the bike either.
If the original owner just cut the baffles out and did nothing about the tuning, that right there will cause a problem. The '06 and earlier bikes don't have closed loop engine management, so there is no automatic compensation to the air fuel ratio. And those older bikes usually didn't run all that great even when fully stock, thanks to the stock tune Harley provided. BUT, you can't just assume a tune is the only problem. There are plenty of other things to consider, like intake air leaks, compression problems, ignition problems, etc.. In other words, some basic diagnostic work would be a good idea.
Jerry