So it sounds like you are struggling with the difference between line and instrument level on your outboard gear. Here is a quicky explanation.
http://www.ovnilab.com/articles/linelevel.shtml
Keep in mind that your Carbon Copy is designed to work with low/instrument output devices (guitar) and that your Moog is an EXTREMELY hi output/line level device. What you typically need to do is really dial the moog output way down then feed the output of the carbon copy into a pre-amp/amp to get it back up to line level. Your Rhodes works because it has an instrument out.
When you describe the “high end” problem, it’s hard to tell if you are getting that due to clipping, or because of the normal frequency range of the carbon copy (again it’s made for a guitar). A Rhodes, even though it has a higher register than a guitar, is already greatly reduced high frequency content. Your Moog is sending tremendously more high frequency information at a much higher level.