Hi Ella,
a) I’m not completely sure what you mean here. Do you mean the archive structure of the data in MASS? Or is it some script that is run separately on Monsoon before data is put into MASS? If the later could you point us to the script used on Monsoon or point us to the task that does this in a suite?
b) Coincidently someone else asked about automating transfer of data from ARCHER2 to JASMIN in a nesting suite earlier this week. 
Pptransfer in UM nesting suite. However i’m just thinking now that rather than pfaffing with pptransfer you could try replacing the moo commands with rsync in the archive app to do the transfer. With rsync the task would have to then run as a background task on a specific ARCHER2 login node.
c) Typically people transfer their data to JASMIN, as large amounts cannot be kept on ARCHER2. For long term storage, or data that is not going to be used immediately, data should be migrated to Elastic Tape at JASMIN rather than left on disk.
Hope that helps,
Regards,
Ros.