Web Forms, Web Pages, Web Sites - Maybe I dont get it!

So I have had issues with my working on my site ever since I upgraded as essenced by my many posts on this subject:
http://forums.asp.net/t/1867273.aspx/1?Validation+Controls+Not+Working
http://forums.asp.net/t/1864056.aspx/1?Several+Issues+with+My+Site
http://forums.asp.net/t/1864395.aspx/1?AJAX+Toolkit+Items+Not+Showing+or+Working
http://forums.asp.net/t/1862215.aspx/1?HELP+ANYONE+No+Answers+to+Validation+Issues+DAZED+and+CONFUSED+
and here are the many issues:
1. The VS2012 editor does not save my toolbox additions or use my formatting preferences
2. If I Create a Web Forms project, I cannot install AjaxControlToolkit or I get an error:
'MsAjaxBundle' is not a valid script name. The name must end in '.js'. The error is not mine because this is the code that is automatically created in the Mas ...