This was a long, confusing post, which I have now resolved, and I thought I would briefly summarize.
I have a number of applescripts that contain the following:
tell application "Finder"
set myFiles to selection as alias list
end tell
When I was using Sierra, the files in the myFiles list would be in the exact order shown in the Finder. Now, with Mojave, the files in the myFiles list are in the order in which they were physically selected in the Finder (typically by holding down the Control key and clicking on a file). This broke a number of my scripts, and I didn’t know how to fix them because I didn’t understand what was happening.