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1) 5.10.x is good for saving JB long-term. Newer FWs are OK too, as long as you keep an eye on sudden OTA updates (then you should install recent hotfix ASAP).
2) Specifically to JB, there no redundant files in the user storage.
3) No. OTA is OTA (over the air), it has nothing to do with manual updates and you should take your responsibility on that side of things.
4) Yes, absolutely.
5) E.g. LibrarianSync if you want to have better collections generation, or maybe Leafpad, or Chess, or kterm Terminal for Kindle. Depends on your needs.
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