Something wrong with references. Try to do this
1) Download Project Manager for version 9.0.6010.0 and go to _EmptyProject\bin folder
2) Compare files from this folder with files in your solution
3) Compare web.configs, maybe you have some old assemblyBindings
Regarding the licence, after an upgrade, you need to download licence for a new version of Sitefinity, the licence file is working only for the specific version.