You made a mistake when you changed references, you should not do that. If you get the latest code form the repository using TortoiseHG all you do is choose the correct build profile (either Debug - MySql or Release - MySql) from the build menu before building the solution. If you did that you should not try to fix it but get the code again instead.
After rebuilding the entire solution you just need to launch the web and visit /Setup/Default.aspx to run the database scripts
If you are using pre-compiled release files there are also no references to change you just replace the data dlls with the ones for MySql
Hope that helps,
Joe