Q:

form: default radio options and branching

This is a form filled out by an agent on behalf of a client. Agent is trained, but we still want to make it accurate and fast.
Question 14:
Is this a Not-For-Profit Business?
3 options (radio buttons):

Not-For-Profit - Registered with CRA
Not-For-Profit - Not registered
For-profit

My q.1: Which order should they go in?
'For-profit' is probably much more common than the NFP. That should place it at the top. 
But this question is about NFP, so this option is the exception (even if it's common).
And it is not really appropriate to change the question to "Is this a For-Profit Business?"
My q.2: We've decided to force the user to explicitly choose an option. So there won't be a default option. 
But the options cause branching. Choosing either of the NFP options will cause more questions to be displayed below, eg.: 'Does this business solicit charitable donations?'
Since there is no default option chosen, it's ambiguous whether or not the dependent content should be shown or not shown before the user has selected an option to the question above.

A:

You are right about the order, but it would be much easier to answer if the options are direct answers to the question that is asked. In this case that would be like:

Is this a Not-For-Profit business?  

Yes, and registered with CRA  
Yes, but not registered  
No

As for branching, you could handle it in either of two ways:   

Show the branched questions, but disabled. Then enable them if they
selected the "enabling option".  
This may be more disruptive to your design, but you could design the form   to show in stages, so you can show the follow up questions
or the next part of the form depending on the answer.

