Could ask EK ticketing office to give you the name/contact detail of the agent in their systems, then contact the agency directly. Depends if it's an internal travel agent for the company or not as to whether your new employer will find out!

As to getting control of the ticket from the agent - it won't happen until you've flown the first sector. Then again, it sounds like you are on a one-way flight...

If you can't get hold of the agent then pay for upgrade at the airport (or on board - but that won't help with baggage) if possible.