All you need to do is use the RUN command after the file has been uploaded.
I would have a look online for a word to pdf creator that can be run with command parameters.
I do a similar thing converting PDF to Tiff files and converting HTML to PDF. I use some products from a company called VERYPDF and from memory they were pretty reasonable.
If the files you are converting are really big you may need to run the process on a background thread.
Drop your code in after this in the webhandler
ReturnValue = PARENT.HandleFile(p_name,p_filename,p_file,p_len)
Eg
Run('c:\PDFtoTIFF\PDF2Img.exe -c none -r 300 -m -i ' & Clip(L:UploadFilename) & ' -o ' & Clip(L:NewUploadFilename),1) !wait for process to finish
If RunCode() ~= 0
Message('Runcode error PDF2Img.exe = ' & RunCode())
End