I’m trying to run my web application on tomcat v6, I was testing it on v7 and it worked perfectly but for this assignment it has to run on v6. When I right click on the web application and run as -> run on server and select tomcat v6.0 server at localhost I can’t seem to click the finish button. Does anyone know why?

It clearly says “The server does not support version 3.0 of the J2EE Web Module specification”.
Just change your web.xml to have the 2.5 version.
Be sure to change the Project Facet too, by right clicking on the project and doing as shown here: