Jason might have said this, but CakeWalk is available for free download, so you can get the software and check it out and see if it does what you want. Sounds like to could do so. Like anything else, you may have to experiment to find the most convenient way of doing things.
Lots of help for CW available via the web.
You seemed to be asking about running one 'job' to split the file into multiple sections? This may not be practical, for the reason that I suggested. MIDI data is handled strictly in the order that it occurs, and various settings (instruments, tempo, volume to name but a few) then affect all the data that follows. If you chop the file up, then various settings will become detached from some (or even ALL) of the notes that they should apply to. Your music will no longer play correctly?
Ask further if you hit any snags.
Geoff