Slow PPr Export with all Dynamic Links

I have very slow exports from Premiere Pro that are entirely made with Dynamic Links to AE (green screen footage).
It's taking about 4+ hours to export a 12 minute video!  Without the dynamic links, it takes about 20 minutes.
I'm on an iMac late 2012
3.2 GHz Intel Core i5
24 GB 1600 MHz DDR3
NVIDIA GeForce GTX 675MX 1024 MB
OS Yosemite
Footage is 1920x1080 .MOV with H.264 Codec, Linear PCM
Footage is on an external HD
Project file is on main HD
Writing exported file to external HD
I've followed several troubleshooting tips including:
Uninstall and re-install CC 2014
Clean adobe media files
Check permissions on all folders
Switch Open CL to Software Only
Unchecked "Display out of sync indicators for unlinked clips"
Disabled "Show Duplicate Frame Markers"
Disabled "Show FX Badges"
I've also tried changing the location of where the final file is written to.
I've also tried this on my MBP with 2.3 GHz Intel Core i7, 8 GB RAM and AMD 6750M
Same results.
Any ideas? Am I missing something obvious here?
Thank you

Hi Matt,
Try this: close After Effects when rendering in Premiere Pro.
Thanks,
Kevin

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