The author wrote an FAQ several years after the original story that answers most of your questions. https://www.ibiblio.org/harris/500milemail-faq.html
"Should have been 6ms instead of 3 for the ACK to come back? Yes, sorry, it was too boring to add"; "Should it be much more and variable because of the routers in between? Yes sure, I probably pinged them and added up the delays"; "Shouldn't plenty of deliveries have failed for destinations much closer than 500 miles? Yes sure, but that must have been the limit..." Etc.
> "There are a number of destinations within that radius that we can't reach, either, or reach sporadically, but we can never email farther than this radius."
"The secret here is the kernel will always round 3ms up to at least one whole tick, 10ms."
Interestingly, not covered in the FAQ.