General help

I think you are talking about a Moodle Quiz, and not a Questionnaire -- can you verify that.  If so, it's best to post your question as 3 separate questions in the Moodle Quiz forum. But here's my take:

is it possible to set some kind of limit to protect confidentiality so that it defaults up to the next level of grouping

I'm not sure what you mean by this question : (

Is it possible to make the words "grading method" disappear from the top of the exercises asmine aren't really grades - I suppose I could just replace those words with blanks 
in the language area but not sure of other impacts of doing so

There is an old discussion about that, but I recommend you post this question in the Moodle Quiz Forum to seee if there is a more recent solution.

Is it possible to not show the competency numbers on the learning log as they cause confusion.

When you say "Learning Log" do you mean the student view of the gradebook? If so, you can go to your gradebook's Setup View and you can click on the Edit icons beside each competency  and 'hide' them so they don't appear to the students -- if you don't see hide in the drop down, then click on Edit-Edit Settings and click the  checkbox option to 'hide.' But, you also need to be aware of other gradebook settings, as doing this may hide the final grade if there are hidden items.