Not sure if these belong here, since it's more nitpicking, but here goes.
Where exactly was that well? Who got John out of it?
How did Eurus get off the island?
How did Eurus keep footage of Moriarty all those years?
Did Smallcroft ever get anywhere?
Ok, the answers to those questions request some imaganation, but I think a have an answer to most of them (although not everyone will be satisfied by those answers, I know):
We can see in the whole Sherlock/John/Lestrade scene in the end that the well was quite close to Musgrave Manor. But then why didn't they find Victor? My explanation is that the well was hidden between a thick hedge or thick bushes back when Sherlock, Eurus and Mycroft were children an nobody except Eurus knew it was even there. Probably the former owner had built it secretly so it didn't apear on any map or blueprint. And as the children had been playing a lot around the house, the searchdogs would smell Victor all over the place, not just around the well. The well was covered so they couldn't hear Victor crying for help if they weren't standing quite near the well. And he probably stopped crying quite soon for lack of oxygen or exhaustion. Of course in TFP the well could be seen quite well, but Sherlock didn't look for it, he went straight into the house and then to the graveyard.
Who got John out of the well? I guess Eurus wanted Sherlock to find John. She had left the rope and the key to Johns chains beside the well or told Sherlock where to find those objects. Sherlock first threw the rope down to John and then the key so John could open the chains himself. I like to imagine that the key was tied to a string, too, so there wasn't any risk of it getting lost between bones . . .
How did Eurus get off the island? By helicopter, just like the rest of the staff and visitors. Either the pilot was one of Moriarty's people or she had manipulated him into helping her. We don't know, but she was basically running Sherrinford, so it can't have been too difficult for her to also manipulate a pilot into helping her.
How did Eurus keep footage of Moriarty all those years? Online storage. We know that she was allowed internet access to help Mycroft predict several terrorist attacks. While she was online, she could easily have installed an e-mail account or some cloud storage service to which Moriarty could send/upload his video files.
Did Smallcroft get anywhere? I think he answer to that question is best left to fanfiction