OK. After about a week of double checking paths and filenames over and over, combing for typos, and anything else that would explain why some scripts work and some don’t…I finally resolved the problem. I renamed the troublesome scripts, created new fresh text files with the original script names, copied the exact contents of the original scripts into the new scripts, and made them executable. Now they suddenly work just like they should.
It seems not all text files are created equal, especially those that I created on a windows machine and sent to the Pi via sftp. For some reason this resulted in files that wouldn’t execute even though they were executable, and instead resulted in “filename not found”, even though I could see the file right there in the folder.
Now I can go about adding some more options to emulationstation like raspi-config, RetroPie-Setup, software updates, reboot, etc. Next I would like to figure out if I can have emulationstation launch different xsession/DEs. I can skip running startx and run xfce4-session instead and that works..but so far no luck with startlxde or lxsession unless I change my default DE. It seems like I should be able to run one or the other without having to change the default.