Hello Kristi,
...when you upgrade to 13485:2003 (from ISO 9001:1994), you have to do several things:
One of the first things, you have to switch to a process-oriented system. There is a lot of literature (and threads in this forum) which can guide you, how to establish processes in your company.
I think, this could also help you to simplify your system.
On the other hand you have to fulfill the requirements of 13485:2003 which are especially designed for manufacturers of medical devices.
If you already follow 13485:1996, there is less work to do, but you will have to establish ~30 documented procedures and implement a strong system for quality records.
In "Annex B" of 13485:2003, there you find a comparison between 9001:2000 and 13485:2003 which can help to find out the additional working-items you have to implement.
Another hint could be ISO/DTR14969 (you can buy it at
www.aami.org), which is a "guidance on the application of ISO 13485:2003"
To the referencing thing:
You could try to use the index of the Standard and make a matrix (e.g. an Excel Sheet) in which you show which requirement of the standard is implemented in which SOP, and which SOPs belong to the same processes. Or you start on the process-landscape and start referencing top down from there.
regards~ghw