Questions ( we have a few )
1. You mention that the 'customer' has access to authoring applications ( Word and Publisher ) and I assume some manner to send / upload / FTP the PDF files they create - yes ?
Do you offer some online instructions that might help guide them on what to do ?
Do you offer blank templates they can use to fill in / use ?
What are you using today ?
Are you imposing the PDF files ( if so, what are you using ? )
What are these being printed on ( example, if these are 8.5 x 11 finished saddled stitched booklets created by folding 11x17 sheets in 1/2, are you printing on 12 x 18 and trimming ? )
Are these self cover, or are you using a different stock for the cover ?
If I had access to a clever programmer type, I might consider using Enfocus SWITCH.
http://printplanet.com/forums/enfocus/20032-flow-questions-powerswitch
Exporting to PDF and then using something like Quite Imposing might also something to investigate.
Many PresWise customer ( I work for PressWise ) build online Wed2Print storefronts for this sort of "please upload you PDF into our template" user experience - not sure if that is something you would consider.
If you are prepared to do a deep dive, you could build you very own
Self Publishing, Book Printing and Publishing Online - Lulu type online tool - while that sort of project might sound massive - you always need to ask "what if i have to double or triple my monthly through-put?"
Several third party storefront systems ( Like Pressero, PageFlex, PageDNA, Red-tie.com ) use our API and send via SOAP a 1 up multi-page PDF files that are multiples of 4 with an XML data file and we convert this in PressWise into an 2-up multipage ( but imposed PDF ) - the XML also contains the Quantities, Bill to and Ship to and all the other things you need to process and order.
Not trying to 'sell' you a PressWise system, just trying to help you understand that this can be as automated and 'look Ma no hands' as you are willing to program.
Good luck - hope you find something that fits your budget.
FYI - back in 2002 I worked for Enfocus, and what you are talking about was done - by Microsoft - for RR Donnelely - by Microsoft's Colleen Isabel - at Microsoft - on a Macintosh! She used Enfocus PitStop and Quite Imposing - to create the manuals for Word ! Each country had to localize the manual into Japanese, French, Russian, etc.. and they would create the RGB PDF files and send them in, and she would convert from RGB into 2 color PDF files ( Black and Spot Blue ).
No idea what they do now ( not even sure they print manuals anymore )