It would help to know more about the type of After Effects projects you're working with as well as if you're using the multiprocessor render settings?
In general though, anything using the Ray Trace render is going to crawl on Open CL; and as the mac pro currently doesn't come with Nvidia as an option we're all SOL there sans for buying an external thunderbolt enclosure and dropping in a card (serious waste of $ IMO). Adobe has acknowledged in other threads they're abandoning the ray trace renderer in favor of the Cinema 4d integration.. but again even that still seems to run better on CUDA than Open CL IMO ( I have a hackintosh at home running a GTX 660 TI that blows away my mac pro with dual D700's here at work, not to mention our older mac towers with a quadro are running laps around this trash can with anything ray traced).
So, yes in its current state After Effects and OPEN CL on the trash can is a very bad combination that can be helped by not using the ray trace renderer, but there's really not a lot of options until Adobe optimizes AE for Open CL or Apple starts to offer Nvidia as an option. Build a hackintosh, or go to windows would be the extreme solutions.
Windows is not really the extreme solution anymore with Adobe. Adobe performs better with the hardware options available on PC especially the new Haswell E X99 platform. AE is mostly all CPU processing and ram. Those D700 cards have little to no impact. If you have to keep the Mac then I suggest getting atleast 32GB of ram. If you don't I suggest you look at X99 with DDR4. The 8 Core Haswell E chip is king right now with performance for both AE and Premiere CC 2014 along with DDR4 which has really opened up the bottleneck for GPU acceleration. Nvidia cards ie Cuda still performs far better with Adobe as well or is the only acceleration for AE when it's actually used.
It sounds like you both are saying that the higher end graphics card I purchased with my mac pro is a waste of money for what I'm using it for. (My AE projects are cartoon style animations -- no Element 3d or Cinema 4d integration.)
Would you recommend purchasing a mac pro with the least expensive graphics card and replacing it with a NVIDIA card? I also plan to beef up the machine with RAM from Crucial.com.
What are your thoughts on the processor? 3.5 GHz 6-Core Intel Xeon E5 More cores or a stronger processor? Again, thank you BOTH SO MUCH!! Really appreciate your thoughts!
Sorry, I'm out of the loop on the newer chipsets so would have to defer to others in that respect. There's a lot of reading to be done on multicore rendering in after effects; but you're best off running some test renders to see if its helping or hindering your comps and then base your decision for number of cores vs core speed on that. Either way multicore rendering does require a lot of RAM. You should be getting OK render speeds if you're not using the ray trace renderer, certainly should beat out the old box, that might be something to look into.
I can't advise using those thunderbolt pcie chasis to add an nvidia card to the new mac pro trash can; the sonnet ones we bought have been finicky with our AJA cards and I can only imagine a full graphics card under load being worse performance wise.
I built my hack a few years back on an ivy bridge i7 with 32 GB of ram. They have some newer guides for hardware choices and methods at http://www.tonymacx86.com/home.php
Although my build has been extremely stable, I will caution that putting together a hackintosh can be quite a pain even if you're an experienced system builder / knowledgable with *nix. If Windows is an option that can be considered, I've heard good things about the HP Z series workstations but Quadro cards seem overpriced IMO compared to the Geforce series for the cuda cores / ram size (though purists will surely encourage you not to go the budget route).
. What are your thoughts on the processor? 3.5 GHz 6-Core Intel Xeon E5 More cores or a stronger processor? Again, thank you BOTH SO MUCH!! Really appreciate your thoughts!
Just for interest here are my results on a PC at the same speed with six cores versus four cores.
"Here are the results of our PPBM6-DE export on the CPU only-centric MPEG2-DVD timeline. And remember the i7-980X is a much older generation.
Quad Core i7-4770K @ 4.2 GHz 635 seconds CS6
Hex Core i7-980X @ 4.2 GHz 540 seconds CS6"