The user has to see all the options so they can choose those that are appropriate, right? I am assuming the following as I don't know the content:
(1) Nesting or grouping won't make anything easier for the user.
(2) Nesting or grouping may be harmful and give you biased responses.
(3) The options are only text and short.
When there's a set of values that you can't explicit show on the screen because they are too many, you can create a modal window completely dedicated to see and to choose one or more options. It is recommended when there is a large set like yours.
The navigation, that consists in going through a set of questions, will momentarily be interrupted so the user can answer that specific complex question and then he will be back to the default flow. A modal is designed for that. It really fits your case.
Finally, this solution also works nice with the concept of a web app.
The interface may look like this:
After closing the modal window, consider giving the user a teaser that indicates that the question was answered.