After you beat Darkrai do some guild jobs for about 2 or 3 days then Manaphy will come back and do another 2 days and Manaphy will discover a island paradise you will be able to go there then you completed the side story
Darkrai
lets you see darkrai in Pokemon mystery dungeon 2
Yeah Darkrai is in the Dark Crater dungeon on floor 13
lets you see darkrai in Pokemon Mystery Dungeon 2
never in history
miracle sea b3f or crevice cave b2f
Yes but after you complete the game. Including darkrai.
Darkrai probably has an advantage over you, or you are just EXTREMELY unlucky.
go to darkrai level and beat darkrai
It depends on Darkrai's level the higher the level the more HP.
No.
Unfortunately, shaymin and arceus don't appear in Pokemon mystery dungeon 2. It has every Pokemon from bulbasaur to darkrai, but not those 2.