I've worked in documents with 650 pages and 300+ linked graphics without much lag so it is not outside the realms of possibility. Linking the graphics made a big difference though so I can understand why you were finding it slow.
Anyway, if you want to continue down the path of separate docs, you will need to configure the headings numbers for each doc. Remember not to refresh the styles from the template because that will reset the heading numbers.
You will also need to configure the 'start at' property for page numbers for each document (if you want the master TOC to be correctly numbered). You can fiddle the field results but the TOC can't be fooled.
And for the Figures and Table numbering, you can use the method described on
http://word.tips.net/T001843_Automat...Documents.html.