I got this sorted. what I had to do was go into my project right click, add reference to go assemblies - extensions and there were two dll files listed under Microsoft.mshtml. I hovered over each of them and seen that the path of one was
c:/program files/Microsoft.NET/Primary Interop Assemblies/Microsoft.html.dll
and
c:/program files/Microsoft Visual Studio 12.0/Visual Studio Tools For Office/PIA/Common/Microsoft.mshtml.dll.
The refernce my project had was the second one in visual studio - I changed the reference to the one in Primary Interop Assemblies under project properties I went to the publish tab and clicked on the application files I set publish status to include. Then I went to project properties/references and double clicked on microsoft.mshtml to open its properties, I set 'embed interop types' to false and 'copy local' to true (as copy local was grayed out to false).
after this I uploaded it to my clickonce server and was able to download and install it.