What I don't get is why these installation scripts never acted up like this in OS 3.9.
I dont know... it always works for me ;-) Without seeing an install script it is difficult to say why it fails. It is also possible there is a bug in the Installer util. Not likely but Installer tool is relatively new in MorphOS.
OS files are also located differently in MorphOS. Maybe Magellan installer is looking for LoadWB command in SYS:C which it cant find there. Or run prefs application from SYS:Prefs. I never had Magellan on my OS3 so I dont know.
As for copying Magellan II over manually...
...aside of the Opus directory, what other files will I need (aside of the MorphOS addons). Also will I just duplicate the Dopus section from the user start up script to the MorphOS one?
You must correct paths before duplicating, of course.