I had work in an eLearning Company that develops Moodle eLearning system and courseware for corporate in Australia and current I am doing a fair bit of freelance work developing Moodle LMS with custom functionality, plugins and custom themes. I had build custom reporting, performance review plugins, performance competence check plugins and even external payment gateway to the system and much more.
Based on your project description, those requirement are fairly easy to implement. Most the feature already exist within the LMS itself when you install Moodle. It would only require configuration and setup.
As for the theme and the certificate that come with Moodle are just plain and simple design, which I would recommend to create a theme and design that suits your brand which I can develop based on Moodle clean theme. I have heaps of experience developing themes and certificate's theme for companies.
If you are interested feel free to contact me and I will put together a detailed scope for the development of your project.