If the engine is offset, you can try hanging the bike from both ends (centerline, top of tubes and steering head) without wheels, but with the engine. Test battery position, fuel tank, oil tank, anything you can...to see if it can be made to hang perfectly vertical. Then you will know if you can live with the offset engine. Don't mount the wheels when you do this...the extra weight will fool you...making it seem like you're closer to correct, than you actually are.
The wheels are spinning, at speed, and don't count as part of the balanced mass pulled 90 degrees to gravity. When speed gets high enough, as we've all tried on motorcycles, you can hang your weight way to one side and the bike doesn't even tilt...but that doesn't mean it might not wobble!
I'm going to have to do the same thing on my project, because the engine had to offset about an inch to make everything come together.
Regards, JimL