I know it has been a while since the last post, but just for what it's worth...
I scan lots of documents to PDF, and I use Acrobat Pro to OCR.
However, there are a number of OCR apps out there for Mac, and another possibility is to use one of those and create Folder Actions which would automatically open any new file in the Scan folder in the OCR app, run OCR, and re-save the file.