That is a much more organized thought process than I had when I made mine. 
It looks good to me and seems coherent enough. 

I think that you should allow for the possibility that a note may have more 
than one question associated with it, and that a question can be associated 
with multiple notes. That could probably be done by giving each question a 
field that contains a list of all of the rowidex values for the notes 
associated with it. It may be a good idea to have the ability to add tags 
or something equivalent to each note to allow searching for notes/questions 
on specific topics.

Since deleting a note breaks indexing I was trying to use in 
http://inmysocks.tiddlyspot.com/#Note%20Taking%20Test%202 I made an 
action-increment widget in the MathyThing plugin to increment the id but I 
haven't gotten around to making a version of the note taking that uses it. 
The widget doesn't have an option for leading zeros, but I don't think that 
would be too hard to add. The plugin would benefit from the ability to give 
a date/time or other format to be incremented so I should probably do that 
anyway.
If there is a button to add a new note/question as part of the view 
templates, and that button was the only thing used to add them, then that 
button could trigger the incrementing each time it was pressed but some way 
to detect when the template is used would be better because it would help 
avoid duplicate ids. 
As you said, the prefix part can be done using WikiText. And the prefix 
would probably be a good way to distinguish between 
classes/projects/whatever is being tracked. (The MathyThing plugin is here: 
http://inmysocks.tiddlyspot.com/#MathyThing%20Plugin I updated the 
documentation a bit so hopefully it is actually understandable now.)

I don't think there would be many new things required to make the backend 
part. The view editing ability and the drag and drop list sorting would all 
have to be implemented, but the way you have it laid out the backend looks 
mostly independent of the display methods.

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