HI, I think I would put all the assignments in one category called 'options'. Then get Moodle to do some calculatons on the grades to make sure the correct number displays in the category total.
Here's an example
max(item1, item2...) means the catory total is the maximum number of item1, item2 etc where item1 etc are assignments.
Where you have 2 assignments in one choice, just replace the 'item1' part with sum(item3, item4) for example. Then it will add the grades from assignment 3 and 4 together, and if that addition is the higest number, it will be displayed as the total.
In your case of course, most of the assignments would keep a score of zero (assuming they only do one choice), so you just want the totals from the option they choose to apear in the category total.
You will probably need to look at what each assignment is 'out of' to make the numbers they add to the gradebook work with the rest of your assignments to give a final course grade.
I think that's about it. The calculations in the gradebook are a powerful tool that gives you lots of options. Look at this page for more info...this link is for Moodle 2 but I don't think it changed from 1.9 to 2.0+. http://docs.moodle.org/20/en/Grade_calculations
Paul