Now, I've replaced ob, but I haven't replaced oa. When the game opens, I hear the original opening game music but then when it gets to Bombing Mission, I hear the file I've replaced it with (which is Dark Messenger from FFVII DoC btw). That's what you want to happen, right?
My "Playback Options" are as follows:
"Loop custom files" is ticked (yes)
"Resuming" is set to none
"Mute midi on custom playback" is ticked
"Maximise midi on song not found" is ticked
"Emulate ramps" is ticked, but "delay stops" is not
"Obey stop" is ticked
I doubt this matters, but my "midi device" is set to Creative SoundFont Synthesizer
Although shamefully, I do have issues of my own with these settings. You know that sound you're supposed to get when you're on the field and you encounter a random enemy? The sound you get as soon as the battle music starts, while the screen is spiralling inwards? Well, I don't hear that for some reason; I only hear the battle music. Also, whenever tracks fade out, my replacement music files fade out really quickly and after they fade out, I faintly hear the original midi version playing for like, a half a second before that too fades out... it's kinda hard to describe it.
EDIT: I just listened to your version of J-E-N-O-V-A for the first time and dang, it's good!! Very well done on that one!