Is there any chance you can have the documents scanned at higher resolution? Low res documents... I hate to tell you this, but to have them at all usable, you're gonna be retyping the entire contents. For example, most OCR software, even the most "powerful" will have trouble telling S from 5 and 1 from l if the document is low resolution.
Yes, I think you're going to have to go with PDF. The only other solution I can think of would have parallel unformatted text and scan files, which sounds like a maintenance headache to me. Acrobat has some built in indexing capabilities, but I suspect your needs exceed that. What about a single site Google search once you've got your PDFs uploaded?