So you are planning on putting SCORM objects into Moodle Lessons ?
I don't think the scoring would be able to pass from the SCORM object to the Gradebook if you do that
As for Lesson navigation, you can use the menu to enable Students to navigate to pages, and using a simple Continue button is simple, but works well (although branching is more fun )
Lesson
How to upload multiple swf files in a lesson
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