I agree with Rick, line up the axle to frame FIRST. Body being off center or whatever is a well known 'secret' concerning body alignment on replicas. VERY typical for it to be off to one side. It's one of those things 'we' don't like to talk about and it's common to a LOT of makes. You can't really 'see' it, unless your looking for it. You can MEASURE it and once I discovered it on my Excalibur it ate away at me all the time. Even though none of my friends ever noticed the off set, unless I told them.
You will find similiar body slightly off center on a lot of Detroit cars as well. It's the nature of the business I guess.