if I replace the first box with a straight pipe, will this allow the enginge to breath better?
Boosting performance, or will the back box, cancel it out?

Replacing the front silencer with a straight pipe will improve breathing, but only a little. For noticeablr improvement, you should also opt for a rear silencer that's a straight-through design.

On a NA car you will loose power! - it's not as simple as removing restrictions as on a turbo car.

Right! I didn't notice you had a non-turbo car! In that case exhaust modifications aren't worthwhile, unless you buy a complete performance exhaust system that's designed for the non-turbo c900. That way you get better flow with still enough back-pressure to allow torque remain the same.