I imagine the three checkboxes for each question are mutually exclusive? If so, do you have code behind them to ensure this? If not, may I suggest either you use option buttons which can easily be made mutually exclusive without code, or to use a single togglebutton, which can have three states corresponding to your n/a,yes/no. This last would mean you only have to look at as many controls as there are questions to get a score.
I've started a bit of exploration of this but need to see some feedback to be sure I'm not on the wrong track.