Thank you for your post.
Well, nearly all the programs you mentioned is possible to disable easily. Please use the WBStartup+Prefs program or just remove the applications manually from AmiKit:WBStartup drawer. I think it is still better than to install missing proggies from the scratch, you know.
With regards to Directory Opus Magellan, I think it's worth to learn how to use it. You can always press the HELP (or PageDown) key to get a help on opened Magellan window. If you decide to use Workbench instead, please follow this link:
I am thinking about creating some instructing videos to help newbies use the Magellan effectively.
AmiStart is really easy to configure. For example, you can use its drag&drop features to add or remove entries. Just disable auto-save feature before you start experimenting :) Read more in the manual located in AmiKit:Utilities/EXPANSION/AmiStart drawer.