if the wheels are lined up, then I would check the neck area. CJ frames have been known to crack under the neck if they have been crashed or otherwise abused hard. if it starts to crack they can tweak out.
also check for twist in the front end (a bent tube is usually the cause). tape a straight edge (like a 12" ruler) across the centers of the upper tripple bolts and site with the front axle to make sure they are parallel. and as mikeo (he pops up at the darnedest times) suggests, swing arm bushings are a possibility. the bike may hedge one way on the gas and the other way off the gas with slop in the swing arm. a loose rear axle will do the same thing. let us know what you find.