empeg-preinit v4 is available.
It now sorts the scripts, so you can be sure that N00mountfs is run before N99emptriv or whatever. While it's solely an alphanumeric sort, I would still strongly suggest using the two-digits-in-the-filename sorting method. (Not to mention that it still requires the N and M initial characters.)
It also now refuses to execute scripts that are not marked as executable. This makes it easy to temporarily disable scripts. It also makes it very easy to accidentally make them fail to run when you want them to. Before you install it, make sure that all of your scripts are executable, otherwise your telnetd may not start and you'll have to hook it up to a serial port.
(Actually, you could just change the mode via kftp, but I like to exaggerate.)