What did you do for the motor/frame/swingarm setup? I see your "oops" photo showing them not line up, but no more photos to elaborate.
Did you remove bosses from the cases? What about the alignment issue?
I think this is the photo you're talking about.
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Found a good welder thanks to Artful and had him do a bit of cut & paste on the frame.
This photo should illustrate the problem better (this is before doing any work).
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I took care of the engine cases with a cutter wheel and narrowed them down to the necessary width for the SBK swingarm to fit.
EDIT: Found where I went over these issues on my build thread:
http://www.ducatimonsterforum.org/index.php?topic=46971.45