Wii won't read GameCube games anymore!

I installed homebrew via Stack Smash, and I thought it caused my Wii to stop reading GameCube discs, so I removed it. But when I play Super Smash Bros. Melee, at random times, I still get the "disc cannot be read...consult the GameCube manual" screen. Sometimes it's after the intro, sometimes it's when I click to change the rules, but usually it's after a match is over. I have evidence that the disc is fine, and the system is messed up.

1. The game doesn't crash on an actual GameCube.
2. Every function in the game works fine, but the Wii sometimes just stops reading the disc.
3. The game never crashes during a match, so it maybe it only crashes when a big chunk of data needs to be loaded.
4. Wii games work on the Wii just fine.

I have a few questions:

1. Is it possible that the HBC damaged my Wii, even though I removed it?
2. Is there a safer way to use homebrew?
3. How do I fix this?

To answer your questions:
1. No, the HBC itself does not affect the ability to play games. I don't know if you installed anything else but it is most likely just a hardware issue.
2. The HBC is safe.
3. As I said it is likely just your disc drive being weird. You could try using DOP-Mii: WiiBrew Edition to install the latest version of MIOS (which is what allows Gamecube games) and see if that changes anything.

I dusted the openings with an air can. It seems to be working fine.