Manually creating a WAD file is no longer necessary with the new web-based randomizer! These instructions have been maintained here for reference, but you should use the website to generate a WAD file instead of this manual method.
These steps are for injecting a randomized US ROM into the US WAD file. This process will actually also work for the Japanese ROM/WAD, however the Auto Injector tool makes this more convenient because of the lack of compression, so just use that method instead.
For obvious reasons, we can't tell you how to get this. Suffice it to say, you need to find the WAD file for the North American Super Mario RPG Virtual Console release and download it.
If you don't already have it on your SD card, download the YAWMM.zip file from here: https://code.google.com/archive/p/yawmm/downloads
Unzip the file, and copy the apps folder to the root of your SD card, and merge it with the existing one. Basically you want the WADManager folder to be inside your apps folder.
We need a specific compression tool to properly compress the randomized ROM. Download this particular tool here: http://www.mediafire.com/file/kmikp03e57ccsto/gbalzss.zip
Extract the contents to any directory on your PC.
If you don't have it yet, download the ShowMiiWads editor from here: https://code.google.com/archive/p/showmiiwads/downloads (latest version as of this writing is 1.4, x64 is for 64-bit systems)
Extract the program to any directory on your PC.
Run ShowMiiWads.exe. The first time, it will show a disclaimer. Change the option to I accept and take the risk of Wad editing features.
IMPORTANT: If this is the first time you're using the program, you need to generate a common key in order to do basically anything with the WAD files. To do this, go to Tools -> Create Common-Key. Type the text it asks you to type and press OK.
You should have an empty window after setting up ShowMiiWads. To add your wads to this window, go to File -> Open Folder. Then browse for the folder that contains your wads. By default, the program should remember this folder and keep it open in the future.
You should see your US wad listed in this window now. Right click on the wad file and select Extract -> To Folder. Choose a folder on your PC to store the unpacked files. I recommend creating a separate folder somewhere convenient specifically to store the unpacked wads.
You should now have a folder in the location you selected with the same name as your wad file. Inside this folder are a bunch of numbered files like 00000001.app and so on. The one we're interested in is 00000005.app which should be the largest of those files. This is the one that contains the ROM file for SNES VC wads.
Go to Tools -> Unpack U8 Archive, navigate to the folder where you just unpacked the wad, and choose the 00000005.app file. Then choose a folder to extract the contents of this file to. For convenience, you can use the same folder this file is currently in with all the unpacked wad files. It will end up in its own folder and won't interfere with the repacking process later.
You should now have a folder named 00000005_app_OUT in the location you selected. This folder contains the raw files that were ultimately packed inside the wad. From this point forward, you can keep this folder around for future randomizer seeds and you won't have to repeat any of the previous steps.
Copy the randomized ROM you have generated into the same folder as the GBALZSS tool we downloaded in step 3 above.
We're going to use this tool to compress the ROM, but it's a very simple command line tool. If you can run a command prompt, do so in the folder where the gbalzss.exe file is located as follows:
gbalzss.exe e <input file> <output file>
If you're not comfortable with the command prompt, I've added a file called compress.bat to help with this. Open this file in Notepad or any text editor and change the file contents to match your input and output files as above, then double click on the file in Windows Explorer to run it.
You should now have a compressed ROM file, for example I used smrpgu.<seed>_compressed.smc in my case.
Move/copy this compressed ROM into the 00000005_app_OUT directory you extracted in the previous step. There should be a file named LZ77JCBE.rom which is the compressed US SMRPG ROM that comes in the VC wad. We want to replace this file with the compressed randomized ROM we just moved in here, so delete the existing file and rename the randomized file to the same name, including changing the extension.
Go to Tools -> Pack U8 Archive -> With No Header and select the 00000005_app_OUT directory where you just replaced the compressed ROM with the randomized one, then choose a location to save the new file. The default name is something like 00000005_app_NEW.bin and we want to keep that for now. When asked if the new file should be LZ77 compressed, select No.
Go back up to the folder where you unpacked the initial wad files. Delete the existing 00000005.app file and rename the new archive you just packed to 00000005.app to replace it.
NOTE: Choosing to replace the existing 00000005.app file when packing the archive doesn't seem to work, so you need to save it with a separate name first and then replace the existing file.
Go to Tools -> Pack Wad and select the folder where all the 0000000X.app files are located where you first unpacked everything. Save the new wad file wherever you want, but I recommend saving it (with a different name of course) in the same folder where your other wads are.
OPTIONAL (RECOMMENDED): Your new randomized wad file should appear in the main window list of ShowMiiWads if you put it in the same folder as the other wads. If not, hit F5 or go to File -> Refresh and you should see it. You should notice that it has the same title as the original VC wad. This means the channel will have the same title once it's installed on your Wii. For convenience, I highly recommend right clicking on the new randomized wad and selecting Edit Title, and changing the title to something with the seed number in it so it's easy to recognize once it's installed. There is a pretty short length limit, so for example something like "SMRPGU <seed>" works well.
In the root of your SD card, create a folder called wad if one doesn't already exist. This folder MUST be named "wad" exactly!
Copy the randomized WAD file you generated in the previous step to this folder, and insert your SD card into your Wii.
Load up the Homebrew Channel, and open YAWMM.
Select IOS249 as your IOS, and leave "NAND Emulation Device" disabled.
Select your SD card as the location where your WADs are stored, and it should list the files in the wad folder we created earlier.
Select your injected WAD file you just copied to this folder, and select Install and it will install it.
Exit the Homebrew Channel and go back to your Wii menu, and your randomized WAD should be present in your channel list with the custom title you entered! Enjoy!
OPTIONAL: You can get a SNES to GameCube converter to play with your actual SNES controller: http://www.raphnet-tech.com/products/snes_to_wii/index.php