Uh... that is just a guess right?

Ok, I finished the game right? Now, lemme get this straight, you get fragments of your soul back right? And you have to build up the rest because it got ripped apart due to the processes earlier in the game, in result, you will become more powerful than you used to be, due to the ongrowing wisdom, I mean you become a better person, you complete your soul composition, and some freaky guys at the end become fearful and someone said that he will still be doomed? BTW, who are those guys?

This is the father of all spoilers, and I may begin to sound like a lawyer at some point.
Most of your soul, apart from the small part (the 'you' in the interactive dream) that stayed defiant against Bhaal (your instinct), was torn from you by Irenicus. When you killed Irenicus in Suldanesselar, your soul couldn't pass on into death, because it was bound to two people. You and Irenicus (the two with possession of said soul) were taken into a limbo state to compete for the soul. You fought Irenicus and won (I hope), rendering him soulless and dead. Then you returned to the prime material plane, soul intact, though probably a fair bit worn out from all the trouble.
The cowled men in the end sequence were old worshippers of Bhaal. The prophecy was that once every Bhaalspawn was slain, their souls would manifest and give rebirth to Bhaal himself. The worshippers are afraid that you are getting too strong to be defeated, thus rendering the resurrection of Bhaal impossible.
A'ight?

WOW. Just what I needed!!! Thank You! And oh btw, can you email me if you have, the Infinity Editor. Thanx!

Ah... the second part is, yes. Pretty damned good guess, though, wouldn't you say?

Damn, Armisael, I almost believed you for a sec. I was thinking, where the ■■■■ did he get this info from?? But it does sound good!

Your character has to go through those tests to learn about himself. Irenicus probably did similar tests but chose all the evil results. I believe I had a similar theory as Armisaels on the cowled men in another thread about the end of the game and what may be in a sequel. It's probably lanquishing on page 40 or something by now though. This was a couple of weeks ago. I'll try and bump it if I can find it.