The other option I can think of that might work, depending on the initial format of your spooled files, would be...
to copy the raw spooled files to a single PF, using the CPYSPLF command (being sure to specify *FCFC during the copy). Then you could CPYF from this PF back to a new spooled file, which could then be indexed (to create the PDF bookmarks). This is assuming that there is some unique value at the same location of every page to use as a key/bookmark tag.
Dig Deeper on Printing on iSeries
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