yeah! THAT's the idea!
It should actually be EASIER than what you were doing, because you get to use some of it over again, and you don't have to think up as much NEW stuff!
OK, now that the motif express is running, I have a whole new set of thoughts:
1) I notice that a lot of your backing tracks have cool drum fills. It would be interesting to hear you mimic the cadence of the drums in your riffs (not the whole song, but here and there as an accent). It would come across as though the instruments were answering one another
2) Now that you've established a THEME, also consider VARIATIONS on the theme. For example one of the times you might add a guitar harmony to the recurring passage to make it slightly different
3) other variations on a theme might be to use MIDI (which you can control note for note) to add other instruments echoing the theme.
I liked that a lot. You are quite the tone-meister