I always prefer to do replication on a per dataset but you can do it at the root of the pool as well, just make sure you choose the recursive potion. Also, make sure you have a backup since moving everything to a single drive is risky if that drive were to fail.
I never move the apps, I just rebuild them when I setup a new pool, but they do have a new app moving feature in 2025.10 that makes that easier. The shares will get auto destroyed when you remove the old pool and will have to be manually recreated in the new pool.