Programatically insert Random Security Identifiers (RSIDs) into Word2003?

[unprimary]

I wrote code that generates two versions of a document based upon two
snapshots of data and then uses then uses Word's merge feature to
merge them into one. It works great most of the time, but sometimes
the merge feature makes quite bad errors like moving half a sentence a
couple of pages away and putting it in the middle of another sentence
based upon a single word in common.

The documents consist of dozens of identically formatted sections as
illustrated:

Document Version 1 Document version 2
Sect A1 Sect A2
Sect B1 Sect B2
Sect C1 Sect C2
....
Sect X1 Sect X2

Differences in section B1 should only be merged with section B2, but
sometimes Word shows something in say section D1 as being inserted
into section B2. Section pairs like A1 and A2 have identical
headings, so I thought that Word would not "find" changes accross
sections.

Is there any way I can make Word do the merge without errors? Can I
programatically enter RSIDs (Revision Save IDs) into the documents for
Word to recognize? Is there anything I can put in the documents for
Word to use when it does the merge?

I am using Word 2003.

Thanks,
Mike