Sometimes you have to step back from the world of pixels and voxels and look at the big picture. If the components had very high detail on them - as in, enough to require machining with a 1/16" bit, then that would be one thing...but machining a model that is 12' long is something totally different. Running a 1/4" ball (and probably even 1/8" - but more likely 3/8 or 1/2") will get you where you need to be on that model. I would not pay a lot of attention to the 'jaggies' at the model boundaries, as your pics show - but instead, rely on good clean vectors and a 2D profile to clean them up on the machine.
No matter what you do there is always going to be some disparity between 2D (the profile) and 3D reliefs when machining. Use it to your advantage.
I would also cookie-cut out a section of your full scale model by drawing a 12" square and machine that to give you an idea of what you'll get in the tangible/real world. It's too often that we want super-tight precision with these projects, only to find we will never achieve it because of the table being off or material warping or backlash etc anyway. Your test cuts will give you more info to go on that anything anyone could write in advisement.
-B