You missed what I think is the big one:

4. Continued access to the Black Sea. Russia needs a warm-water port, so their navy doesn't get stranded in the winter. Geographically, both Crimea and Ukraine are critical for that purpose. If those countries turned NATO, and NATO went aggro then Russia would lose that access. So it is critical for them that they secure it. And securing it after Ukraine joins NATO is an invitation for WW3.

You may be thinking "NATO is a defensive pact, they will never aggress." That may seem self-evident to you, but it's a lot harder to accept on faith for the country that happens to be NATO's raison detre.