Well, lessee, all these questions about souls now! The way it works is this:
Your first playthrough, you get one preset soul, as well as two random souls. In RS (which everyone seems to have), you are obligated to get GutsSoul in the first tournament. Afterwards, you have a chance at getting Wind or Roll Soul in the Eagle Tournament, and Search or Thunder Soul in the Red Sun tournament. The second time around I'm pretty sure you get Fire and the other Eagle Tournament Soul; The final time around you get the other Red Sun soul.
So, for you, Hao, even though it's supposedly random, your first time around since you got Guts, Roll, and Search Souls. You should get Fire and Wind Souls your second playthrough, and your final game should end you up with ThunderSoul. That's if my assumptions are correct; I think they make you wait for the end of the third game before you can get to the secret end-of-game areas, and that means waiting for the final tournament before you can access it. Please note, though, that it's all random. I doubt that busting level, HP, or anything else has any bearing on Soul distribution, since I ended up with Guts, Roll, and Thunder Souls. By the way, a word of advice: ThunderSoul, for all intents and purposes, STINKS.
As for your question, ProtoSoul, I don't think so. I think you get your 3rd Tournament Souls in the first and third playthroughs. Then again, I'm not dead sure, so you can always hope, right?
Hope that helped some!