Regarding using Exalate for migration purposes, please note that while Exalate is a synchronization solution, and therefore it can be used to copy data from one system to another - a typical migration functionality we do not entirely encourage this as the tool is not optimized for this use case.
If you still wish to proceed using Exalate for your migration, I believe that the steps in your description should work. Nonetheless as per the above I would rather recommend:
Perform the projects migration with the JCMA
Do a clean up of the connections from JSM B to obtain the mapping
Use this mapping to do the bulk connect.
Please let me know if you have any doubts regarding this and I will gladly assist you.