Urgent Need: Prolonged Export of After Effects Motion Graphics video

I agree with @Mylenium. Even exporting a ProRes file directly out of After Effects will give you significantly faster render times than going directly to MP4. It takes much more horsepower to render frames, then compress them to H.264 than it does to encode an intermediate format like ProRes. I recently did a test on a shorter UHD animation; it took 9 minutes to export H.264 (with Hardware Acceleration disabled) and only 90 seconds to export to ProRes. So even making that extra, much larger, intermediate format and then converting that to a MP4 will save you loads of time.

An image sequence, however, is a good idea in case something goes wrong or you can only export a certain number of frames at a time. Try TIFF or compressed EXR instead of PNG, as After Effects is notoriously slow when it comes to encoding PNG sequences. 

File sizes don't matter. Even a 1.7 MB file will expand to a few hundred megabytes of data per frame when decompressed. and that likely is simply the issue. Even in 8bpc mode you may be exhausting your 8 GB of RAM or whatever you have and on top indeed the limted transfer bandwdith of your external storage may figure in somewhere, too. You're likely also not helping matters along by encoding with VBR and hardware acceleration. At the very least start by rendering out an image sequence directly from the AE render queue and encode it later. Otherwise there's a good chance only massive restructuring of your project will bypass some of the performance issues, but that would require much more specific info on what's actually going on.

Mylenium