Sometimes you have to know what you're looking at to arrive at the solution.  I didn't know what I was seeing until I did the MeshLab on your objects and zoomed in.  Still wasn't sure what had caused it, but I could see the multiple faces clogging the model.

Carry on!

The black circle shows co-joined facets.  Looks like a weld that didn't take, or two objects that were booleaned that were overshot a bit.  Either way, there are other things that are there as well and most of them look like this. This one shows a few more issues.

The green and yellow show separate objects that seems to be joined together in a single object.  This is not watertight, therefore non-manifold.

As I don't use blender, I can't tell you how they got there, but they need to be fixed before it will be sliced correctly.

I know, I'm not telling you anything that you don't know... sorry, maybe I can take a deeper look at the model tomorrow.

Try porting the model into MeshLab.  Go to Filters->Cleaning and Repairing->Select non Manifold Edges.
Check Preview, then Apply, then OK.

Switch the view to Flat Lines (toolbar, looks like a mesh with blue facets in it.   Rotate the model and look for red/pink areas.  These are non-manifold parts.  Load the model into Blender then fix the facets and edges that were red/pink

It takes some doing, but you can clean up a mesh pretty easily.

I have no problem seeing what is non-manifold but what I can't tell is WHY it's non-manifold. If I can't tell what is causing it I can't fix it. One object is symmetrical with one part having a non-manifold place on it and the other identical half does not.  MeshLab does seem to be a pretty decent program though.

The files are above in post 6, both in .stl and .blend formats. I can still email to you if you'd prefer though.

Switch the view to Flat Lines (toolbar, looks like a mesh with blue facets in it.   Rotate the model and look for red/pink areas.  These are non-manifold parts.  Load the model into Blender then fix the facets and edges that were red/pink

It takes some doing, but you can clean up a mesh pretty easily.

The second is the exported .stl while the first is the original file.

Manx: I appreciate the program recommendations but I've already gotten comfortable with Blender and finally figured out how to do the operations that I required. It's actually quite spiffy once you get past the learning curve, plus it's open source!

jon_bondy That's good to know. I was needing to do it in program as it is many pieces than need to be scaled to the proper size together.

I seem to have figured it all out now, except for non-manifold parts. I used cloud.netfabb.com to fix them but it butchered one piece and messed up the scale. =o\

I don't use blender and don't know what it is, but the program you download for the printer will have a program that will allow you to scale, rotate, and place an object however you need it to sit on the bed, so don't worry about if you're not modeling it in the position you need it for printing.

If you can fit the parts onto the bed shown in the program then it should be fine other than possible issues with blobs and or strings, and maybe uneven bed temps as you start placing objects further from center, (this was the case for SD2, I don't know how the bed is built with the SD3 so maybe this won't be an issue).

Would the attached file print properly?

How do I scale the model to control print size in Blender?

How should the pieces be oriented in Blender to result in the proper facings being toward the build platform?

Are multiple large-ish parts in a single print okay?

I appreciate any help!