A 3 MW reactor puts out a hell of a lot of heat, and without the benefit of air-cooling in space, I'm not sure what exactly you would do with all of that waste heat. Consider how massive the space shuttle orbiter's radiators were (they are on the inside of the cargo bay here: http://i.stack.imgur.com/Flgzb.jpg ), and all of that is only capable of shedding waste heat in the amount of ~6 KW! We can put a much more capable reactor into space than we can possibly cool, so we haven't bothered. Cooling is the real problem. The total mass of the radiators and the structure required to support them ends up being way more than the reactor itself.
So for good long distance transportation in space, not only do we need a working, efficient emdrive, but we also need better power generation that is much more efficient from a waste heat perspective. These are really hard problems.