Here are some points of interest for you:
Glossary of terms
3.1-4.1 System Mod Guide
4.2 Mod Guide
As far as all the programs used in the mods, they are found in the Mod Guide [depending on what system menu you have on your Wii now] and will be in the download links of those guides. Please read everything more than once, so you know exactly what you are doing.