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Kodax has a bundled software/scanner that scans docs to jpg, pdf or tiffs. For converting from MSWord to PDF I would look at GNOSTICE.COM components to do the work. It needs some programming work though.
You can integrate the process by writing the output into a memory stream and have it integrated with your EMR and save it to database by loading it from stream. GNOSTICE has all these capabilities. If you need more info just continue this thread with your questions.