What’s the best way I can enjoy the story up until Dragonflight, so I can get ready for War Within? Do I just go from area to area and play through their storylines?
Also, is there a difference between Horde & Alliance anymore? Can I do LFR and play with either side? 
As long as you’re not 70 yet, you’ll need to follow the campaign through the zones, yes. You can ignore most side quests, if you only want to reach max level. Once 70 I’d take a look at a guide because it gets really confusing with all the max level campaigns that will pop up. Horde an Alliance have the same story, for LFR I’d wait for Season 4 as the last season will breathe new life into the previous raid wings. You can’t queue up for LFR/LFD cross faction, sadly, only join custom groups.
Do you mean the story before Dragonflight or the story during Dragonflight?
You wrote you are back. When was the last time you played?
Go in order of expansions. Avoid Shadowlands.
Only in BfA.
No you cannot do queued content cross-faction such as LFR, but you can do Normal and up cross-faction (for raids) and Mythic and M+ (for dungeons).
You can choose to level up zone by zone, enjoying the vibes, taking your sweet time of it. All of the zones, the campaign, then the Aberrus cave, and finally the Emerald Dream.
No. Not LFR… Yet. but lore-wise, nah. We also got cross-faction guilds now so the faction barrier is getting removed gradually.
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