I may not have the "best" way to inject N64 games but I do know one that actually works without closing hundred times using Injectiine v1.23. The first thing you MUST do is to download the latest Python for this to inject at all. The Second thing you need do is to go to the Wii U N64 Inject Compatibilty page here to make sure the game you want to inject works:
http://wiki.gbatemp.net/wiki/WiiU_VC_N64_inject_compatibility_list
The third thing to do is make sure your "Files" folder have these files in it otherwise it WILL crash.
In case you are wondering what should be in the "Base" folder you can look at the reply I made to caliskier above this post. As for the bootTvTex and iconTex images you can go here for the image templates I used:
https://github.com/cucholix/wiivc-bis
The third thing to do is if the N64 game you looked at in the Compatibility page needs a custom INI file to run then make sure to copy the text into notepad and name it after whatever the name of rom is in the "Base" folder. The location of rom folder in Base folder should like this example: "Injectiine v1.23\Files\Base\content\rom\Unmfe0.443" Once you make your INI file you need to put it in this location: "Injectiine v1.23\Tools\CONSOLES\N64\INIs" Just make sure to make a copy of the original INI file in it instead of replacing it.
Now that all of that is done it's time to use Injectiine! Following the onscreen instuctions you need to type the number 3 like it says for N64 injection.
It shouldn't crash since you have all of files I told you to put in the "Files" folder in the beginning. Next thing to do follow the next step and type in 3 again.
Press any key to continue like it says onscreen since you already supplied everything it needs.
Depending on the title of the game you can use one or two lines for the name of the game. After you enter in the name of the game you can enter in a custom product code.
Next type "n" because you don't need to enter a title id.
Next type in "y" because we just want to inject the game.
Now enter the name of the rom file used by your "Base" folder. The example here is the name of rom in my "Base" folder
After it goes through the process you see onscreen you need to type in 7 because that will grab the custom ini file you put in the INI's folder earlier. The reason why we are not using option 5 or 8 is because Injectiine would always not work for me when I did those options. It only worked when I used option 7.
Now if you want the game in Loadiine format type "n" but if you want the files for installing the VC game on your Wii U type "y". After the process is done it should say injection complete. If you decided to make files for installtion you need make a folder in the root of your sd card called "install" and put the folder in there finally use an installer called WUP Installer GX2 install the VC game on your Wii U. If you made Loadiine version you need to make folders titled "wiiu" and then "games" on your sd which should look like this on your sd example: "F:\wiiu\games". Finally copy the Loadiine folder made in the "games" and use Loadiine GX2 to play it.
I hope this helped in someway if this still doesn't work and you want N64 games on your wii u you can google a certain iso site ment for wii u and you should find a thread with a collection of VC games which has plenty of N64 games that work.
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1. Yes certain roms can be injected in fact someone made A SMO64 injection on a certain iso site ment for wii u which you can google to find.
2. You need to download Python to use the .py files which will let you inject games
3. Look at the reply I made to caliskier above here for what the "Base" folder is.