I've gone back and tried applying all transforms for both the rig and the mesh, still no dice. All that did was scale the mesh down 100 when imported to UE4, unfortunately...

I tried clicking "Normalize All" and Limiting the total to 4 for all groups, then exported and did the retargeting, sadly this doesn't seem to have fixed anything and the issues still persist. I really appreciate the suggestion though, thanks!

The blinking is fixed now! I exported with "Apply Modifiers" unchecked and then reimported after the initial import, that fixed the issue!

Would circles be the issue?, because I think I have a large number of those

This is similar to my case I think, though I do not have any bezier curves in my project

Thanks for your time and help, I appreciate it

Will do in future, though I stupidly thought you could open 2.8 files in 2.79 so didn't make a backup. I have now tried exporting at Collada and Alembic. Neither worked as I hoped, the Collada kept the materials, lost the textures and messed up the geometry, and the Alembic lost all materials and texture but kept the geometry, and lost animation data, I suspect the Collada lost animation data too, though did not check so cannot say for sure