I'll skip the first two stages since it sounds like you've already got them covered and it's not too hard to get past with just the basic tips (use strong high level Pokemon, use super effective moves, keep full restores on hand, have Green Canari Plushes, etc.). The main potentially tricky part is just to run when 50% Zygarde uses Land's Wrath; don't stop to command your Pokemon to attack.
It's nice to withdraw your active Pokemon with the ▼ button before a major attack if possible, but you really need to prioritize taking care of yourself in this battle, so just ignore your Pokemon if you're struggling to move fast enough. This applies to all parts of the battle. You can continue fighting if your Pokemon faints but not if you do, so this is the time to use any Max Revives you've picked up. At this point your Pokemon should be able to take at least a couple hits anyway.
When Complete Zygarde jumps out of the arena to use Core Enforcer, immediately get to the edge of the arena. You've already noticed the two gaps in the Z-shaped attack; they will always be on the lateral sides of the diagonal stroke in the Z, so if you can recognize this pattern and predict where the safe zone will show up while Zygarde is still drawing the Z, you have a couple extra seconds to get there. You need to roll when Zygarde attacks, even if you're not fully in the safe zone. The reason why the NPCs tell you about rolling is because it gives you invincibility frames, which can let you avoid taking damage even if you are technically being hit by an attack. This isn't always useful in some of the other story battles, so you could have gotten away with not doing it thus far, but it makes a big difference for this fight. It can be tempting to keep dashing in order to try to make it into the safe zone if you're almost there but rolling is pretty much always the better option if you're falling short.
You should also spam rolls when Zygarde is using Land's Wrath. Since this attack radiates inwards and eventually covers almost all of the arena, it's really difficult to avoid getting hit just by running away. The strategy here is to roll into the attack (towards the edge of the arena) rather than away from it (towards the center of the arena), so the next attack doesn't appear underneath you when you finish your roll. If you time your roll right, you won't take damage as you pass over the burst.
Thousand Arrows is an easier move to deal with, just make sure you are running when you see Zygarde starting to use it. An easy mistake is to try to use these moments to tell your Pokemon to attack, but this makes you sluggish and you don't want to be caught stuck in place when the arrows come down.
In general it's good practice to keep your distance from Zygarde since it can stomp to hit a small radius around itself. This is a good battle to play defensively and conservatively, which could be a bit different if you're used to being able to sweep opponents quickly. Most of the challenge in beating the Complete form is in managing your timing rather than how strong your Pokemon are.
