Chris,
I think you have a few choices. First, leave the holes off center, it really isn't going to make that much difference. (Except to to you , naturally, since you know the @#$ things aren't right.) Your method is certainly one alternative (did you happen to cut those holes and gave the pieces laying around?), and laying up some fiberglass to plug the holes is another. I'm afraid that the only way I would order another hull is if absolutely nothing else worked after repeated attempts. (That has a lot to do with me being cheap.) I'm also assuming that you have a fiberglass hull. If so, the 'new' one may not be fiberglass. Whatever you decide to use for the 'patching', finishing the patch on the outside is going to determin just how evident the patch is. A good job of finishing would be very nice. Good luck.
- 'Doc