Professional OCR packages usually do PDF files. Your complaint is a common problem. The more basic OCR packages sometimes included as freebies usually (always?) lack that functionality - so you'll have reason to buy the full package.
Chances are you have a basic OCR app already. You might have gotten one with a scanner, especially if one of your scanners is a cut above the bargain ones. See if it will open a PDF file to read the images. If not, save each page as a TIFF or PNG picture - you can do this with Preview, though it will be tedious for 100+ pages. Maybe there is some freeware utility that will save each page as a separate document. Don't save to JPEG - artifacts will decrease the OCR accuracy.
If you do save them manually, make sure the page is scaled up enough so the text is clear. Run them through the OCR program one at a time. Copy the results into a text editor. You should proof it even with clear type - OCR makes mistakes here and there. When you're done with cleanup and restoring formatting, save the editable copy for future reference. Print to PDF and the resulting PDF will finally be searchable. The contents should be indexed by Spotlight too. And that final text PDF will be way smaller than the original.
Edit:
PDF2Image will export a PDF file to a succession of image files.