At the risk of finding out that MikeN teaches heliarc welding at the local trade school, I, having no heliarc experience, am going to venture that the hardness and quality of welds to cast aluminum are dependent on the quality of the welding service employed. If I recall correctly, there is some welded area around one or two of my base studs and those welds are holding fine (I need to "go to film" to cofirm, however).
If your case numbers are already mismatched to your frame, no big deal. However, if they match the frame, and better yet, concur with the original dispatch documents, you would certainly be better off repairing the cases. I know this from experience, now sorely regretting having discarded my original bent frame in an effort to save a piddling $300 in frame straightening cost. I learned too late that the difference in dollar value of the bike is probably close to 10 times that amount.
All this said, MikeN has given you very good advice on the other aspects, even if we slightly disagree on the cases. Filling in one of Mike's unsaid points, cleanout that sludge trap.
Richard L.