Fixed it!So yes, technically the problem is resolved now. However, it took about 3 hours of my life to figure out what went wrong. I figure I can help save other people a headache if they run into a similar problem. Anyways, here's how I resolved it:
Problem: Unable to run the latest bannerbomb or smashstack. Specific games (Brawl and MKart Wii) don't load. Homebrew dissapeared.
After doing a lot of searching I found ModMii, a very cool utility that made fixing this possible. Using it I generated the necessary files to put on my SD card by choosing "Homebrew Fix". By doing so I was able to run the bannerbomb (finally) and get Homebrew back on the Wii. Yes, this step was huge. ModWii also included the Homebrew app "Multi Mod Manager".
Now with MMM at my disposal I was able to investigate what ISOs were active and installed. Using the ISO browser I was able to see that ISO36 (it even told me this ISO is used for brawl, MK: Wii, and homebrew) was the problem. So how did I fix it? Using a utility I found called "NSU Downloader". Using it I was able to get access to a healthy ISO36 WAD, put it on my SD card, and used MMM to install the WAD and the corrupt ISO36 was patched.
So, in closing, MMM is a great debug/repair tool. Get it. Use it. Check the ISO Browser and see if any problems you are having relate to any of the ISO descriptions (mine was with 36). Relating back to my original problem, I'm guessing the Homebrew installation messed up and my ISO36 got corrupt somehow.
PS:
The second you get BootMii running do a NAND backup! I'm doing this right now. It will save you a lot of time and frustration if you do it. I'm sure in the future I'll be happy I backed it up in case this happens again. If anyone has any questions just ask.
Don't link to gbatemp, and don't mention ModMii or MMM again on these forums. --bg4545Edited 1 time(s). Last edit at 02/12/2011 09:53PM by bg4545.