Pencil and paper? My god... Use the reader's highlight function, for crying out loud!
Scan Tailor outputs uncompressed TIFFs and that's why they take up so much space. But don't resize them! Resizing can add antialiasing (blurriness), which doesn't compress well. If you run them through Acrobat (reduced PDF then optimized PDF) they will get compressed. Just be careful not to choose lossy compression because TIFF can support either lossless
or lossy.
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I'm also very concerned about being able to use the new ebooks in the future with little to no additional manual labour done to them. I'm also trying to get this done as quickly as possible, with as few steps as possible, but with good quality - archive quality not necessary, but close to it is the goal.
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Ha! Good luck with that. What I found is that not one format converts 100% accurately. We're in 2012 and you'd think HTML is probably the safest bet. But it's NOT the format itself, it's the software that reads and interprets it! For instance, Sigil has ePub validation built-in. Your ePub could pass and still look completely different on some e-readers! We're back in 1999 where you could look at the same website with a different browser and everything would look different.