REFLECTOR: Leveling: Center Line

Well, it is now clear that my bottom fuselage is somewhat twisted.. in order to get bulkhead locations level side to side.. I end up with a cowl that is 3/4 inch high on one side... Any suggestions? Is this a freak occurance? Also, I went ahead while I had the thing loose again and turned it over and cut out the nose gear door hole according to the factory markings... Cut it perfectly straight... And at a glance it doesn't look like its perfectly centered to the centerline.. Perhaps not crucial.. Do the factory markings tend to be off? It's possible the twist has affected my center line I suppose also.. The way I figure it, even if the fuselage were twisted, bringing it into level at two or three bulkhead locations should bring it to a straight alignment, provided that it is semetrical.. When canard bulkhead and firewall are level the back end is way off.. Conclusion,,, fuselage is Asemetrical.. What should I do?? It's not going to untwist in the air is it?? I assume I'm going to have to just level the bulkheads and worry about the back later... right?