The simplest approach is probably to rename the files to always start with 3-digits. So 1-Title becomes 001-Title, 99-Title becomes 099-Title. This is very easy to do with a script in Linux, and I assume it can also be scripted under Windows (but I don't the details of how to do this).
An approach, that works with an arbitrary order is to provide an .opf file which lists the order of the files. See
ePub: OPF.