It would help if we knew what engine/drive chain system you have. If the engine is a standard Chinese 2 stroke, in-frame, and the drive and driven sprockets are now properly aligned you have a bit of a challenge. You can always space the sprocket futher to the left, away from the hub, but that will alter your chain/sprocket alignment.
It sometimes becomes necessary to off-set the engine to the left. This naturally requires custom engine mounts. That will mean some imaginative metal work and welding.
I have two bikes with 3" x 24" rear wheels and the engines are off-set 9/16" to the left of center.
One other option is to have the rim 'dished'. That requires the spoke be adjusted to pull the rim off center from the center of the hub. A job best left to a good rim/spoke guy unless you know what you're doing.
Good luck.
Tom