The Smithsonian Institution Archives cannot provide specific recommendations for the treatment of your objects. However, the Archives can point you to a number of resources that can help you understand the nature of the problems you described.

If you’re working with papers that are faded, the fading of documents is often irreversible, but it may be possible to enhance legibility through two means:

• virtually, through manipulating high quality scans or digital images shot under visible, infrared and ultraviolet light (multispectral imaging), or simply under visible light, and enhancing contrast and color levels in the digital images using photo editing software;
• physical treatment by a paper conservator to possibly enhance legibility by removing stains such as (body)oils and brown degradation products from the paper with chemical action, thus enhancing the contrast of the ink/pencil and paper.

Sometimes papers have text written on both sides, making it hard to decipher the text on each side. In terms of manipulating images of your papers, it may be possible to enhance legibility through a couple of means, listed below in order of ease and access:

• changing the exposure settings and thresholds on your scanner through the software interface;
• for the thin papers, putting either a white or a dark sheet of paper behind the object;
• Post processing in Photoshop by doing the following:

-Enhancing contrast and color levels in the digital images shot on the scanner or in visible light using photo editing software (changing images to grey scale, adjusting exposure & levels in Layers, using the Photo Filter set to IR in the Filter options, adjusting Threshold so only the darkest darks and lightest lights appear, making 50% opacity layers and layering them over the image background, for example). A graphics imaging reprographic specialist may be able to help you with this phase of the project.

-Make lots of copy layers to play with and save it as a different image in TIFF or PSD format; rather than opening, making changes, and saving the original file as a JPG, which deteriorates over repeated saves. If you find something that works, save it as an Action and run it on the rest of your documents.

-Shoot the images under a copy stand using visible and ultraviolet light with infrared filters and UV filters on the lens (multispectral imaging), or simply under visible light, and further manipulating as in c). However, these are specialty items to acquire and use, and do have particular risks of their own. Iron-gall inks disappear in the infrared, which by playing with contrast levels and the IR filter further in Photoshop (which actually enhances black & white contrast), you might be able to virtually fade back the strike-through of the ink on the verso.

You may be interested in the Walters Art Gallery Archimedes palimpsest project, to give you an idea of what is possible with multi-spectral wavelength imaging, as well as a colleague's blog post on using digital cameras to capture in the infrared light spectrum.