Regardless of the dis-assembly method you choose, you should Pathagorize (neuter) the document as much as possible before disassembly. This will help to assure consistency.
•Convert 'real' names, addresses, quantities, dates, etc. to plain text bracketed variables as possible.
•Denote optional text blocks and create options blocks.
•If you are working on a source document that has 'real' names that run throughout the document, don't forget about Pathagoras' Create Variables Assistant. The Assistant lets you highlight the first instance of the name, and to replace each occurrence of the name with a variable in a single action.
•If you want paragraphs which automatically renumber themselves, you should assign the automatic numbering fields before the disassembly. This will assign the identical auto-numbering parameters needed to insure proper numbering when the disassembled clauses are reassembled.
Here is the most important piece of advice. Don't worry about getting everything right! Because of Pathagoras' plain text underpinnings, you can always 'Pathagorize' some now, disassemble the document, and edit more later after you see some results. And as far as editing goes, you can either return to the Master document, Pathagorize it some more, and then disassemble again, or just edit the individual clauses that you disassembled the Master into. Your choice.