Instead of using the source code from GitHub that was provided in this post, I looked at the license file and used the download link for my current version of Plex.
licenseFile: /usr/lib/plexmediaserver/Resources/LICENSE
transcoderSource: http://downloads.plex.tv/ffmpeg-source/ffmpeg-2018-03-22.tar.gz
I was able to compile in --enable-decoder=h264_cuvid into that version with ease.
I have not tested it as a replacement yet, but will do so later tonight.
