What should I know about running third-party patches and installing OS 3.9?
Before installation, disable or remove any and all patches. This includes MCP, and any non-essential entries (i.e. commands needed for your accelerator are OK) to S:Startup-Sequence and S:User-Startup. Remember to remove any patch programs from the SYS:WBStartup drawer as well. Before enabling your patches after installation, be sure that none of your patches are duplicating new functionality already built-into–or offered by–OS 3.9. Remember that WBCtrl, DefIcons, AslPrefs, and others are now integrated into the OS. You can get an idea of what new functions/features are included in 3.9 here.