I know this post is kinda old, but I can help. The answer is in the partition tool of Wii Scrubber. Simply load the iso in Wii Scrubber. Right click on the data partition. Under Unencrypted Partition, select extract. Create an empty folder with a name you will remember to extract the files to. After the extraction is complete, use your pc's file system to replace whatever files you want to replace. I did one with "thousands" of files and I wasn't about to replace them one by one. Anyway, after you have replaced the files you want though your pc's file system, expand the "+" of the data partition in Wii Scrubber. Create a new folder to extract different files into and name it something relevant to remember. Extract the files partition.bin, apploader.img, boot.bin, bi2.bin, and main.dol to the new folder you just created. Open up the Wii Scrubber partition tool. Load the first five files according to their names partition.bin, apploader.img, boot.bin, bi2.bin, and main.dol from where you just extracted them to. For the last blank, use the folder that you extracted that whole data partition into. Then build the partition and just accept the default name. Go back into Wii Scrubber with your iso loaded and right click the data partition and select load. Browse to where you just created your partition and load it. That's it. YOU"RE DONE! Do with it what you will. Your iso is now patched the way you want it and it was ALOT quicker than replacing each file one by one.
HOPE THIS WAS HELPFUL!
PEACE OUT!!!