The complication is that pageviews are tracked with the Pageview tag, whereas link clicks are tracked with the Custom Link tag. You could set a common eVar with both tags, e.g. to track the page name. But once you breakdown that eVar by the Custom Link name, AA will report 0 pageviews for each Custom Link because it was impossible for it to track a pageview with a Custom Link.
I normally have to resort to Excel for something like this, which sounds ridiculous for something as "trivial" as calculating a clickthrough rate.