I have three SCSI scanners now (Microtek flatbed, Nikon film scanner, Fuji duplex sheetfed which I haven't used yet). I've found that using the standard Adaptec SCSI interface works best; others can be flaky.
I've had good experience with add on PCI USB boards. They're pretty cheap (e.g. 5 ports for <$20), the cables are much easier to deal with the SCSI (more flexible, cheaper, and far fewer versions), and there are no termination headaches.
Consider looking at eBay and elsewhere for refurbished scanners (that's where I got my Fuji). Also, I've seen new duplex sheet feeder scanners at Fry's for much less (IIRC Xerox for <$400).
I haven't yet done what you looking at doing, so I can't help more there. A typical scanner will come with OCR software; Nuance/Scansoft also sells a lot of OCR (newer version of the Caere products) and PDF software.