Creating 3D side by side and saving some time during rendering..?

I've got a 1280x720 comp. It's fx heavy. Rendering the 2D is taking a full day! I've got a fan pointed at the Mac! I'm tempted to stop it, but I need to check for errors before the next step.
I want to export a 3D version. I've figured out how to get two cameras and generate seperate R and L comps. But this is going to take forever!
Now, since my final ouput is going to be 'side by side' (so both comps get squashed up on the x axis and half the data is lost!) is there some way to do this in rendering (output side by side) and save a bit of rendering time? Like render to two frames of 640x720 and not the full frames and then throw away half the data!
Am I missing something important..?
What if I instead choose to upscale to 1920x1080 (keeping the same camera lens angle) to preserve resolution, can I do the same and output straight to side by side without any intermediate render for size changes?
I'm using CS5 on a Mac.
Cheers!
p.s. Have a happy Easter!

Well I did a search for "after effects" +"towel-strip comp" and got nothing! You'll have to explain that a little!
The composition is all done in Particular emitting, in total, maybe 80,000 objects! Here's an early version
If I'm happy with the 'left eye' render, maybe it's easier just to render the right eye and then import, resize, and render again. Do you think that might be quicker..?

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