So, start off going here:
http://smealum.github.io/3ds/
Download the Homebrew Starter Kit and unzip it into the root of your 3DS SD card. It will put a file in the root and make a 3DS folder with other stuff.
Remember to unzip the contents of the Starter folder, not the folder itself.
Also get JK's Save Manager:
https://gbatemp.net/threads/release-jks-savemanager-homebrew-cia-save-manager.413143/
Again, unzip it to the root and it will put everything where needed. Same as before, you want the contents, not the folder it's all in in the zip.
Assuming you're using Ocarina of Time, you need:
https://github.com/yellows8/oot3dhax/releases
Now, put your OoT in your Powersaves and back up your save.
It goes in C:/Users/<Your User Name>/PowerSaves
On
http://smealum.github.io/3ds/ use the Otherapp/robpin tool. Put in your system type (old or new) and the version. Hit download ropbin. It will give you a file, you don't need to save it, just keep it up for reference.
In the zip for the OoT hack, there will be a couple of folders with PowerSaves files. There's two sets, I used the bottom. You may have to try the other if it doesn't work. Go to the folder for the country your system is for, and in it find the file that matches the ropbin file that you have for reference.
Copy that file to the directory of your PowerSaves backups. Copy the name of the backup you had made, then delete/rename it, and paste the name as the new name for the file you grabbed from the OoT folder.
Then when you load up PowerSaves, you restore that file back to the cart.
Then, with your SD card back in your system, load up OoT on your 3DS. Hit A to get to the start, load up the hacked save, and when everything is loaded on screen in the game, hit A. This will boot the Homebrew.
Once in the Homebrew, put your MHG cart in, and go down the list to JK's save program. Select ExtraData, and export. Give it a name and export it.
Now you can pop your SD card in your computer, and run the MHG editor and just load up the exported file, which will be under the SD:/JKSV/ExtData/<Game Name>/<Save Name you choose>
Once you're done, save, then pop the SD back in and just do the same, except Import the extradata.
And you're done.