Set up looked like this

on the left the cube is merged, looks more than fine. on the right in the preview window you can see that it's offset the two .stl files. I thought that might not print out that way, however here's the spaghetti mess that resulted from this

gaps, messy / fused base and many layers were not fully printed correctly.
as for the Frog from Nervous Systems

The raft fused together into this unbreakable mess. The supports (which were probably not needed) looked to protrude through the body somehow. There's also a ton of little curly bits of ABS all over the body, not the smooth print I was expecting, let alone offset like the cube. This was a costly print to boot AND took 10 hours.
First question is why is Simplify3D offsetting the .stl files? There wasn't any mention of needing to adjust them so they fit better. When the two files are merged in the starting window I would expect to see the same showing with the mesh view in the preview window.
second is more with the overall printing - there just seems to be some data lost or scrambled during the printing, no matter if I'm using USB or from a SDHC card.
Any suggestions on settings or guidance would be greatly appreciated - thanks!!