Test Early and Often
You've done everything right — studied up on WCAG 2.0, trained your team members, and scanned your site with an accessibility tool. Yet you just received your usability test results, and they refer to errors that never occurred to you. Unfortunately, this is a common problem, and the best solution is to revisit your site code.
Why All the Extra Effort?
WAVE and SortSite won't catch everything. For example, while WAVE can catch missing form labels, it will not help you detect text that should be marked as a heading but isn't. To catch those slippery accessibility issues, take the time to go through the page code itself, especially in cases that involve your site's functionality, such as keyboard operability.
Start With Template-Level Problems
Keep a list of your site's templates and reusable content modules, and check them first. That way, when you fix these errors, the fix will be reflected throughout the site. Save evaluating body copy and individual downloads, like PDFs, for later so template-level errors don't distract you. When it is time to tackle tougher issues, divide them up among members of your group so everyone can approach the testing with reasonably fresh eyes.
Schedule Your Next Testing Cycle
If your site is brand-new and fully accessible, plan on asking your accessibility team members to scan new and updated site content on a monthly basis at the very least. Speaking of your accessibility team, which you assembled in Step 2, ask them to write down their previous methods and workflow so you can train new team members on the process.