Help with dual extrusion infill

[yonkiman]

I'm trying to print a bunch of trophies for my pinball league. I designed them in OpenSCAD, and printed the first one:

However while I was printing it, I noticed that the infill was unnecessarily complicated, wasting filament, increasing print time, and adding unnecessary filament swapping:

So I made some changes to the design (see base on rear right) so that there wasn't much if any overlap between the two sections:

However that didn't work as expected. Since there's a 3 attachment limit per post, I will continue in the next post...

[yonkiman]

When I slice and check "Merge all outlines into a single model", I get the exact simplified infill I wanted:

But as you can see above and below, for some reason the slicer adds a layer of green under the letters and in the holes in the text:

If I uncheck "Merge all outlines into a single model", the outside slices well and looks good, but the infill is either:

1) messy (as shown at end of previous message) if I use the solid base model (rear left on image in previous message), or
2) missing, if I use the 2-part base model with the floating ring on top (rear right).

Can anyone show me how to get the outside I want with "clean" infill inside?

I've attached my factory file if you want to try it with my existing models (choose one base or the other), however I'd be happy to modify the stl models if that's what i need to do to print this cleanly. I need to print a lot of these (note that I'm starting with Summer 2016 ) and would like to save time and filament (and reduce the risk of a jam during a filament swap) when I start cranking them out.

Dual Filament Trophy.factory

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Appreciate any help/suggestions!