Recently been watching people playing this, so I have a good idea of what might work here. 

Harry is stranded out in the middle of a hidden Ocean (Think Bernuda Triangle style, ships are unable to get into it. That isn't true, but this fiction for a reason. Let's just say a hidden wizarding Ocean).

The Aurora could be a crashed nuclear sub instead of a space ship, just to keep it more... Human.

Building things could be explained by transfiguration and augmenting those items could be enchanting? That one will be left up to you. 

Yes, Harry can use magic wand leaky if you want, but you can take it away when he gets his wand, something about the bond between him and the wand blocking wandless magic? Again, up to you.

Being rescued can happen at any time after Harry has built a relatively good base.

After some research, I found out that Leviathans are serpents... And the game has Reaper Leviathans... Pet RL anyone?

He can keep his tech when he goes to Hogwarts, on account of them being created by transfiguration and enchanting, in case you go with the explanation.

He won't have the guide that tells him about his hunger and health etc.

He can use the submarines and stuff, but they won't be as hi-tech, try to keep them modern era.

If he finds the island, he can make a base on the island, but he HAS to have some form of enemy on the island, be it an animal or someone who has survived on the island without a base. 

Any particularly wierd marine life can be explained away by it being a MAGIC ocean, or something similar I guess.

Thats all I can think of at the moment. 

Im just gonna fill this in with another chapter from one of my fics. FYI, none of them will line up with each other, it will just be random chapters.

A small boy, about eight years of age, was running through the street of Privet Drive. This was in a vain attempt to escape his cousin, Dudley Dursley, also eight years old. Whilst these boys were cousins, they couldn't be more different. Harry was a short for his age, scrawny child, with emerald green eyes and pitch black hair. He wore glasses and baggy clothes that were several sizes too big for him. Dudley however, was of average height, overweight and had malicious, deep blue eyes and blonde hair. He wore a white shirt and tracksuit trousers, with the shirt struggling to contain his girth. Dudley was the resident bully, who would constantly beat on Harry when he was bored, leaving Harry with bruises, cuts, scrapes and broken glasses.

"Okay Harry, just a couple more streets and we can get away. Don't look back, you'll slow down. Just keep facing forwards. Yeah, that's it! Just keep running, just keep running, just keep running, running, running, what do we do? We run, run..." Harry continuously encouraged himself, attempting to make his legs move faster. He passed through the end of Privet Drive and saw the library merely a few metres away. He immediately ran inside and tried to calm his breathing. He walked through and looked for the kids section so that he could read something whilst he waited for his cousin to grow bored of looking for him. 

"Okay, let's see... Skuldiggery Unpleasant, Diana Chicken, Perry Johnson. Nope, nothing I havn't already read... Wait, what's that? What does MC mean? Let's read that one shall we?" Harry spoke to himself, looking through the books on the shelf. Picking the newest one, he opened it up and began to read.

'MC is the standardly used abbreviation of Minecraft, a game created by the mundane peoples of the earth. What they do not know, however, is that the creator of the game, code name: Notch, is actually the one and only practitioner of Miner Magic, allowing one to manipulate their surroundings to their will using only their magic, fists and what they can craft using their magic. While this magic seems generally useful, though not amazing for battle, there is one advantage that Miner Magic has over all other branches of magic. This is the ability to use Miner Magic without a tool to channel magic through, such as a wand or ring. This allows for several distinct advantages against opponents who rely solely on magic based on a foci. For examples of these advantages, go to the listed pages.'

Harry was in shock. 'What is this book? Magic? Notch? What is a foci? What do I do?' Harry then turned the page over to see the contents page. Listed on the page were several titles with numbers beside them. Harry read down through the contents, surprised at what he could see.

'Contents
Introduction 1How To Use 2-5Basic Recipes 6-15Advanved Recipes 16-25Basic Combat 26-30Advanced Combat 31-35Mobs 36-46How To Mine 47-50Redstone 51-60Visual Effects 61-63Death 64-65'

Harry's eyes bugged out when he saw the last one. 'What does it mean by death? When you die, you die right? Whatever, I'll start out with how to use.'

'To use Miner Magic, one must first realise that everything is simply a tool for you to use. Everything from a sword to a flower can be used in a way that will help you, be it in battle or simply to make things look good. The next step is to access your magic. This can be done by meditating. Many people cannot access their magic on the first try, so don't be discouraged by failure. In fact, use failure as a means to push yourself further. Finally, one must punch a tree. Don't be skeptical, this is an actual part of the magic. If you are able to access your magic on the first try, this will be much easier, however this should still work, either with or without accessing your magic on the first try. This final part all comes down to belief. Your magic is sentient, and will follow your belief in an attempt to emulate what you want to happen. Have no fear if the first punch doesn't work, it will over time if you believe and continue to punch. You must continuously punch the tree that you have chosen. If this works, your vision will change to view everything in the form of cubes. Don't worry, this is a natural part of the magic. Another side effect is that, what has been termed as a 'hot bar', will appear in the bottom of your vision. This will be where you choose what you are holding. If you did this correctly, a block labelled 'wood' will have appeared in the first 'bar'. You can then open your 'inventory' by clapping and clearly saying inventory. This will open the inventory and allow you to use a two-by-two crafting area, along with thirty open spaces in your inventory. Each space can hold a maximum of sixty four of any item, excluding a select few.'

Harry nodded, deciding that it was worth a try at least. He looked through the library for books on meditation techniques. When he finally found one, it was getting dark, so he walked up to the front desk and presented his library card. "Can I take out these books please?" Harry asked the librarian. She was an old woman who had volunteered for the silence. She just nodded and forgot to mark the books with the stamp. Harry took this as good for him, and began the trek back home, holding his books underneath his shirt and hoping that his relatives wouldn't notice.

"BOY! WHAT TIME DO YOU CALL THIS! I'VE BEEN WAITING FOR MY DINNER FOR FIFTEEN MINUTES LONGER THAN USUAL, ONLY TO FIND OUT THAT YOU'RE UNGRATEFUL ARSE ISN'T MAKING MY DINNER! GET INTO THE CUPBOARD AND STAY THERE! YOU AREN'T GETTING ANY FOOD FOR THREE DAYS!" This was the sound of the Vernonius Durslius in it's natural habitat, attempting to berate a disobedient pup for being late to make dinner. All that the creature managed was to turn his face an intriguing shade of beetroot purple and to raise his blood pressure. Harry immediately ran inside his cupboard and winced as the door was slammed and locked behind him. Harry then grew excited. "Yes! Now I can practice my meditation and try and access my magic!" He exclaimed quietly so as to avoid enraging his uncle any further. 

Harry began to read the meditation book, looking out for any tips that could point him toward successful meditation faster. As he read, he began to drift off. He fell asleep reading the meditation book, unaware of the consequences of staying up past midnight.

Harry awoke to complete and total silence. For three seconds. "BOY! IF THIS HAPPENS AGAIN, I WILL PERSONALLY KICK YOU OUT OF THIS HOUSE YOU UNGRATEFUL LITTLE BRAT! WE HAVE FED, CLOTHED AND RAISED YOU OUT OF THE KINDNESS OF OUR HEARTS, AND YOUR UNGRATEFULL LITTLE ARSE CAN'T BE BOTHERED TO WAKE UP AND MAKE BREAKFAST!" Harry cowered in the corner of his cupboard, waiting for the moment Vernon would leave the cupboard and let Harry continue his reading. "YOU WILL STAY HERE UNTIL DINNER, WHICH YOU WILL MAKE WITHOUT A PROBLEM OR YOUR ASS IS OUT!" Harry nodded fearfully, before wincing as the cupboard door was slammed shut.

Harry then remembered where his book was and began reading again. After an hour, he finally decided to practice meditation. He calmed his breathing and focused on one spot, the top of his head. As his breathing slowed even further, he began to drift off, before his eyes snapped open as he saw the cupboard fade around him. He watched on as the area around him became a void of sorts, leaving him to float without the knowledge of what was up or down. As he looked around, he heard a voice, small but wise, telling him to imagine what he wanted to appear. This caused him to look around, before shrugging and trying. 

"Okay, so if I imagine a large mountain surrounded by lakes and villages, that will appear, right?" As Harry said this, he noticed the void begin to fill in with land, before the land formed into a large mountain, surrounded by small lakes with clear water and small villages. He saw several people begin to walk around the villages. He walked up to one and tried to talk to him. He turned towards Harry and looked into his eyes. Harry began reliving one of his memories. Specifically when he found the Minecraft book. He shook his head a he heard a sound similar to lighting and looked toward the mountain. He walked toward it and noticed a railway with carts that lead into the mountain. He got into one of the carts and began the journey into the mountain. When the cart stopped, he froze in amazement. Before him was a giant ball of glowing light. He realised that this shouldn't be possible, as it dwarfed the mountain. It was then he realised how deep into the mountain he was. He walked up and touched the ball, and immediately felt a rush of strength fill his body. He began to wake up, unaware of the snake-like face with red eyes that watched him.

"THAT IS IT BOY! YOU HAVE DONE THIS FOR THE LAST TIME, GET OUT OF MY HOUSE AND STAY AWAY FROM THIS FAMILY YOU UNGRATEFUL BRAT!"