Error with azure project

You need to specify all your setting names (without values) also in the Service definition file in the ConfigurationSettings section.

So your ServiceDefinitionFile should look like:

<ServiceDefinition name="ServiceLayer.Azure1"     xmlns="http://schemas.microsoft.com/ServiceHosting/2008/10/ServiceDefinition" schemaVersion="2014-01.2.3">


 <WebRole name="ServiceLayer" vmsize="Medium">
<Sites>
  <Site name="Web">
    <Bindings>
      <Binding name="Endpoint1" endpointName="Endpoint1" />
    </Bindings>
  </Site>
</Sites>
<Endpoints>
  <InputEndpoint name="Endpoint1" protocol="http" port="80" />
</Endpoints>
<Imports>
  <Import moduleName="Diagnostics" />
  <Import moduleName="RemoteAccess" />
  <Import moduleName="RemoteForwarder" />
</Imports>

  <ConfigurationSettings>
  <Setting name="Microsoft.WindowsAzure.Plugins.Diagnostics.ConnectionString" />
  <Setting name="Microsoft.WindowsAzure.Plugins.RemoteAccess.Enabled" /> 

     .... and so on (all your settings here

  </ConfigurationSettings>
   </WebRole>
  </ServiceDefinition>

EDIT:

The same you need to do for your Certificates section.