You do not have to Unstaple 400 pages, but use a split function 4 times to separate into 5 documents and store them individually, but with the same indexing info, perhaps add a new index feild (Document Section Number?) and have indexed with 1,2,3,4,5 for each document.
If you want to keep it as a single document, you could still split it in 5 parts, and then add to the tray 4 specially created 'separation' pages (as PDFs - use printing from MSWord to Docuware Printer) which will contain some unique text such as "Document Separation Page", and have all 9 documents stapled in order of alternating document parts and the pages. Store resulting document.
Then when you have the document found by search, you could use the Docuware Viewer "Start Fulltext Search" and "Fulltext search continue" tools to locate your bookmarks (Searching for "Document Separation Page")