I have the newer wii with the usb (not gc controller) slots. I soft modded it using letterbomb method. Got homebrew channel and whatnot. I downloaded some free games on Homebrew Browser and my Wii Remote wont work. Is there anything i can do/download to fix it? And can anyone give a simple instruction or link on how to play games from sd/usb? Thanks guys!
The newer "TR" remotes came out about 2 years ago. At that point, any homebrew older than the TR remote would not know how to use the TR remote, and it just shuts off and you can't use it.
Many apps that were in current development at the time recompiled using the latest dev tools and TR remotes work just fine.
2 years later, any old apps still floating around still can't use TR remotes, and likely never will. Your only bet is to find an old remote (non MotionPlus Inside remotes) to use for the older homebrew.
As for playing games from SD/USB check NTFS guide or FAT32 guide (links in signature). Currently can't use GameCube without the ports, but a future project still in development may make that possible with other remotes. If you are interested in this, you'll want to use FAT32 guide and format to 32k clusters if you want to be future-proof. The guides will show you how to format and prepare your hard drive and show you how to install games to the hard drive.