I don't know which software you intend to use, but I'm pretty knowledgeable about Cakewalk/Sonar/VST plugins (using midi, of course) and whatnot. Not sure if that helps <i>you</i>, but, like Marlin, I would also proffer my arguably limited knowledge on the subject.
About Penultimate Toccata (which was nice to listen to- the first half sounded reminiscent of Final Fantasy, at least): I've been listening to a lot of songs on these boards lately, and while it doesn't happen too often, I notice that sometimes the .mid files have extended periods of silence after the song proper ends. While I don't know exactly why this occurs, I know at least how to fix it. If you open your sheet music view (or page or bar or whatever your program calls it) and go to the last note, you might find that it's exceptionally long for some reason. Just replace it and (for good measure) stick a rest in there. That's usually what works for me, anyway.