My thanks, Hedley, for all of the suggestions. In the end the new version of Apache was causing us too many problems, so to get a clean install I reinstalled Ubuntu 12 and WeBWorK 2.7 from the Live DVD and went forward from there. I upgraded WeBWorK to 2.9, got the new Ubuntu HWE stack, but did not upgrade Ubuntu from 12.x to 14.x. I'll deal with upgrading Ubuntu and working with the new version of Apache later as we needed to have a stable system quickly. Happily I had kept tarballs of all of our courses, as well as a dump of the database, so we did not really lose anything important in this process.