Q: Building complex MIME messages

I've been writing a little application which will help me move from my
current remote mailbox format to a different format, mbox.

My 'example' source message is the following

                                   1
                                 /   \
                                2     3 (file)
                             /     \
                            4       5
                           / \     / \
                          6   7   8   9
                        (file) \       \
                               11      10
                                 \
                                  12

Does anyone have any grand ideas how I might go about doing this? 
Current I'm going through each message in turn and recording what the
MessageID(s) of its children and prepending the previous entry such that:

1    2,3
2    4,5,3
4    6,7,5,3
6    -,7,5,3
7    11,5,3
11    5,3
5    8,9,3
8    -,9,3
9    10,3
10    -,3
3    -

 From this, I want to build a MIME message and maintain the hierarchy 
within the subsequent message.

Thanks for reading all this.  Any ideas?  Thanks in advance!
Adam