Seems like I remembered that wrong, Nikola boss can recover legendaries even if you released them but only once. My bad on that part, hopefully you can get help somehow.
If you release a legendary you cannot catch it again via the Nikola boss. Nikola boss can only recover a legendary if you failed to catch it not if you release the pokemon.
You can try to get it recovered by staff in the restore pokemon megathread.
They have been sold already.
The attachments include sold pokemon too, so make sure to click the spoilers to see the pokemon that are still available, you also will find the prices there.
I dont know about a list but I have some things in mind you can do before entering Johto.
Subway quest to unlock transportation for Kanto and Johto later on.
Arcanine mount quest to get a free mount.
Unlock Love Island by doing evolutions and some other stuff.
Complete the Kanto dex and do some evolutions as it helps you out with getting legendary pokemon later on.
Maybe there is other stuff to do but thats what I can think of at the moment. Also everything of those things is optional so its up to you.
Thats because its from a region you have not finished yet. So in your case either Johto, Hoenn or Sinnoh.
To unlock it you have to finish the region the pokemon got caught in.
Gothita and its evolutions can only learn stored power and cosmic power in gen8, since PRO is based on gen7 it would make no sense to make these moves available.
A lot of pokemon can use rock climb too and we rearly need it but we still gut the Abseil Rope Tool. (same for Flashlight and other tools/moves)
So I dont see this as an argument against the suggestion.