OK so I've got good news. I got all of my saved data back! How? Well it seems that the idiots at Nintendo are not only stupid enough to not know how to fix their own system but they also didn't know I could copy the data myself! It seems that when they replaced the motherboard all my data was erased but some part of the old motherboard must have stayed in the system. I don't really know but ANYWAYS... When I got it back I tried to copy the data from my SD card to the Wii. It said I gotta play the game on the system first. Well I was so busy with Brawl I just never got around to it... Anyways so I test it by putting the game in, playing it, NOT creating a new save file, and then I exit it and it worked! I now have not only the saved data from my disk games but also from my virtual console games!
Short version: I got all of the saved data from my other games (which was lost) back.