Most everything runs pretty well, except that After Effects is taking forever to render when using the ray-tracer.
This is a common issue. It is not recommended to use ray-traced 3D compositions any longer, especially if you do not have a qualified NVIDIA GPU (which you do not have).
Don't worry, though. Instead, look into using Cinema 4D Lite for your 3D needs, which is available from After Effects. Choose Layer > New > Maxon Cinema 4D file. If you do so, does Cinema 4D Lite launch? It should. Try it out.
Here's my question, given the below setup, what upgrades can I make to use these programs more efficiently, if any? Should I look at nVidia GPUs and install multiple cards on this motherboard or will my system even be able to take advantage of multiple GPUs in Adobe products with this setup?
Bigger, better, or more GPUs will not affect After Effects performance very much. After Effects is more dependent on CPU power and large amounts of RAM.
Do I simply have my AE settings configured wrong (quite likely)?
Just avoid ray-traced 3D compositions and you should be fine. You may want to familiarize yourself with After Effects, as well. Here's a great place to start: Getting started with After Effects (CS4, CS5, CS5.5, CS6, & CC) | After Effects region of interest
Let us know how it goes.
Kevin, thanks so much! I appreciate the help. Looking forward to getting some amazing stuff from this product. I had read about the Cinema 4D, but hadn't taken the time to investigate it. I'll definitely do that now. Very grateful for your time, friend!