I inject my services into my controllers. The services return DTO's which reside in Core.
The model you have looks good, I don't use the repository pattern but many people do. I is difficult to work with EF in this type of architecture which is why I chose to use Nhibernate.
A possible answer to your final question.
- CORE
- DOMAIN
- DI
- INFRASTRUCTURE
- PRESENTATION
- SERVICES