I scan and upload various land use and financial documents for a county and its townships to the internet on a shoe-string budget - actually, no budget - all volunteer, public service for fellow citizens. This is my prescription:
Stay with your current flat-bed scanner. Do not waste money on a sheet-fed scanner. You do not have nearly enough money for a high-end Fujitsu or Bell & Howell sheet-fed scanner which will reliably get the job done without mechanically screwing up. The pros use high-end scanners because they never screw up and they go fast. Cheap sheet-fed scanners miss sheets or jam up too often to trust them with anything. Make a sign-up sheet for work-study or volunteer students in your academic department to sit down at your computer and scanner and scan the documents into the computer. Give them free pops and gummy bears (slur it so it sounds like "rum & beers") or something similar which won't transfer from fingers to documents. Just take a few minutes to set them up and show them what to do. Keep it simple. Let those empty minds waiting to be filled with knowledge (and beer) do the time consuming zombie work. You should focus your attention on how to put the files on the website.
The scan file format I use is Portable Network Graphics format or PNG format. On average, it compresses black and white graphics 20-25 percent smaller than the widely used GIF format. PNG format is also supported to a basic enough level to be displayed using MS Internet Explorer, Netscape, Mozilla, and other internet browsers.
I use free Xsane scanning software on a linux system to scan the documents. Xsane can be set to scan in line-art mode, also known as black and white mode. This software can also be set to save files directly to disk in PNG format and automatically change the file names using numerical iteration, i.e., file-01.png, file-02.png, file-03.png, etc. without the need for human intervention to change the file name each time. I use a 100 dpi scan resolution setting because documents do not need to look ultra-smooth; they just have to be legible. Anything beyond that is a waste of hard drive space. Using this resolution also means I do not have to spend time embedding the graphic file in html code to constrain its width so it can be viewed on the average 15", 800x600 resolution monitor. I just insert weblinks to the individual, one-page graphic files: "Page 1, 2, 3, 4, ...", with each page number hyperlinked to a corresponding graphic file. Your graphic files will run 15-25kb each. The use of PDF graphics format is a waste of time and space unless a professor gives you a MS Word file of their lecture notes which you can convert directly into a PDF file with embedded text. That is the only case in which I would use PDF over PNG. Good luck.