Alas i have no experience in ModPlug Tracker..
But in terms of putting a song together to be covered, im only starting to do so, and i never felt when doing the intro to Fade to Black that i had a certain bit to start on, its really how the song progresses, the drums are a good start though if it kicks straight into them, but yeah, depending on stops and starts, fills and licks, you should just work with it however you feel most comfortable, and if one way doesnt feel right, it may take a bit longer, but in the end coming off with the best piece is what youre striving for, so experimenting never hurts at this stage

Dont know if that helped at all but i felt somebody should say something, as i highly dislike when people just ignore my threads. Call me attention seeking but hey, why would you post the thread in the first place if not for feedback?
Again hope i helped even a tiny bit.
Megadokyo.