I was always under the impression for things like engine cases (especially from my air cooled VW days) that if you had a damaged case half, you basically needed to replace the entire case, due to slight manufacturing variances in the casting. From what I understand, if you have a shaft that rides on a bore that is shared between both case halves, they may not line up within spec.
Ross or some of the other HD tech guys may be able to support or dispel this.