I read for the day was about how Linux handles runlevel scripts. Good read, and I understand it. Whew!

But I have one question that was not quelled by my research.

Take the name of the /etc/rc5.d/S99firstboot link. Other than simple lowest to highest priority when starting and stopping services, is there a significance to the 99? I see multiple S99* links in /etc/rc5.d, and the only thing that might separate them is the alphabetical order in the start/stop sequence.

Also, what happens if you should not shutdown a particular service when changing runlevels?

No, I don't think so. The 99 just means that it is run after all the scripts with lower numbers.
The reason for the numbers is so that services are started, and stopped, in the proper order because some services depend on the availability of other ones to intialise, shutdown cleanly (eg you can't write something to a log file, if you have already unmounted the filesystem), or work properly.
Yes. But I am not sure that the order is defined as alphabetical or anti-alphabetical or anything else. Maybe there is an RFC somewhere? It is possible that equal numbers could all be permitted to be run concurrently by putting them in the background.
Then you might not be changing the runlevel "properly". This might be something you need or want though, it depends on your circumstances, and you need to be a careful. For example if you wanted to switch to runlevel 1 (Single user) and you omitted to shutdown and kill all running users, or allowed them to login again after they had been killed, you wouldn't be in "singleuser" mode anymore, would you?

However, there will be occasions when you need to start or stop some service running in your current runlevel, that was not defined to do so in the rc?.d scripts. For example, you are in runlevel 3 and your system is not set up to run sshd in that runlevel. You can easily start it yourself with /etc/init.d/ssh start

The only differences between runlevels is which services are running, or not.

HTH