Can't Get SageCRm 7.3c to Install

Recently upgraded from SageCRM v7.2b to v7.3c and it seems a number of things did not install. Tomcat will not run at all. Sage tech support dialed in and they could not fix the issue either. After the install a number of files and program files that should have there are not there.  Has anyone seen anything like this? And yes we did take care of anti-virus and the like. Ran as administrator