D'oh! Apologies to you both. I didn't notice it was someone else offering help.
Rebekah_harper's method of hiding one solid to export the other is one way, and is the way I usually choose for this purpose. Another way is to select all the solids, then go to File > Print > Send to 3D Print Service. In the dialog that appears, select 'Selected' under Print Range, then click Options and in the 'Structure' dropdown, select 'One File per Selection'. This way, separate files are automatically created with '_SolidX' appended to the file name. This is far more convenient than the hiding method when you have many solids in your part.
@t2k3d: I opened your body.ipt file in Inventor and exported the separate solids. I then dragged them into S3D and followed the procedure that I outlined before, i.e. select all the parts and then choose 'Align Selected Model Origins' from the Edit menu. They aligned properly, so we know your construction and .ipt file are good.
So, I have attached both the .stl files knowing that they work. Please try them with your S3D installation. If they align properly, we know it's your Inventor settings or export procedure that is the problem. If they don't align, we know it's S3D. Either way, we should be a step closer to a solution.