1. I would like to scan a huge stack of photos so that I can dispense with the paper - and oxidation, etc that goes with them. I want to know how I can get the best quality result from scanning. Can I scan them all with a high dpi/file size setting and then go back and apply filtering with photoshop - contrast, color balance, etc or am I better off using the filtering when I scan?
2. I have a brother mfc-J5910DW printer/scanner. The only software that comes with it that uses the automatic document feeder is Paperport, which does not seem to save to jpeg. Is there some other scanning program that will let me use the adf to scan photos? The ADF has no trouble feeding the photos through.
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Scanners all "filter" their output. You can tweak the exposure before scanning when you notice something wrong with the preview, but you shouldn't rely too much on what you see in the preview. You really should have your monitor and scanner color calibrated to do any quality work.
If you are satisfied with results one or two notch down from perfection, then the automatic exposure output of the scanner should be fine. You should scan your originals at the highest native non-interpolated resolution of your scanner.
About your scanner, all-in-ones are not quality minded devices, compromises are made in all sections. Depending on how serious you are with your photography, you would be better off with a dedicated photo scanner. Also, JPG is not an archival format, you should save in TIFF.
You can improve the situation with a combination of Vuescan Pro and Adobe Lightroom. Vuescan can output RAW scan files and since it uses the Brother driver it should be able to use the ADF, but check with them.