The others == drMerry?
Well, there are problems, I knew it when I started this question.
But main problem is the false-positive.
This is why the quality-check is a 'helping' function, not a 'dictator'.
Just like the title in series it will show some info.
I think it is a lot of programming, so only start if you're motivated
I think you have to have one thing clear: It is an option presented to the user. The user is not forced to use it to have the benefit of the other functions.
So I can imagine theducks would not use this function because he has to much 'errors' while he uses the index in an other way than the 'normal index numbering' (what is normal...)
But think of the duplicate finder. If I would ask you at this moment to give me a plugin that could do all functions duplicate finder 1.0.2 does, you would say it would be a hard thing to program.
The way you solved that was for a great part by adding separate functions and let the user combine them. (with or without pre filtering the books to test)
I think that is the way you could work at this moment to.
To make it 'simple' you could start with a one-book option. Just select one book (or in left hand one series) en process this.
Give the user an option-screen to select some details (trial and error, only main-indexing, 2digit sub-indexing, 1digit sub-indexing)
That would give a result for the selected series. You could also add an option like last index: #, equals last index
Just some suggestions, but like I said. It may be a long walk so only start when motivated