Strumelia:
1) Am I going to lose the hundreds of major and minor customizations that were done on both my old Core and on so many of my modules? (The customizations were done BOTH via ACP, and directly on the server...both by members of the JR Team and by myself.) What am I in danger of losing and what do I need to especially look out for?
I believe you are using a custom skin? If so no - nothing changes.
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2) would it be advisable to update only the Core first, and see how it behaves for a few days... before then slowly updating the modules maybe two or three at a time and checking that they haven't lost my tweaks?
You can, but I don't think there is a need to. JR 5.3 is not a NEW core - it's new features built on 5.2, so things that were working in 5.2 should continue to work the same (or better) in 5.3.
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3) what safety precautions can I take before updating? Is there a way to revert back if I see the Core update has wiped out lots of customizations, added custom functions, or style tweaks on my site? What's the worst that can happen?
The problem with reverting is that you can't revert the DB changes, so in this case your best bet would be to restore from a backup if you find it doesn't work for you.
We've updated A LOT of sites from 5.2.41 to 5.3.0 - we've seen a couple small issues (mainly around the Marketplace giving you a 404 not found or something - cache reset fixes it) but so far I feel the upgrade is a smooth one.
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Brian Johnson
Founder and Lead Developer - Jamroom
https://www.jamroom.net