Level: Depending on the level of The Nameless One when he faces The Transcendent One (and by extension, TTO's level), their combined levels can easily hit 80 (or exceed it). According to
TTO's stats, TNO has had Cleric levels during some of his incarnations (implying that at some point not all of the gods ignored him as they do now). The actual numbers for TTO aren't especially important, as some of them are impossible for the stated class combination and are inconsistent with established knowledge of some of TNO's incarnations (at the very least, one of them was known to be a Thief). However, the trends they describe (such as the fact that he is listed as having Cleric levels) can be taken as meaningful.
Moreover, I felt a desire to ensure that TNO's classes (whichever they were) would be balanced. However, a 21+ level Wizard would be expected to have epic spells (which TNO shouldn't have).
So, these three factors (TTO had cleric levels, all 4 classes should be balanced, should not be 21st level Wizard or higher) put together lead to Fighter20/Rogue20/Wizard20/Ex-Cleric20. A side benefit is that, assuming his ability scores start at 18 (easy to handwave, since the way TNO gets his power doesn't truly fit into D&D's levelling paradigm anyway, so any attempt to stat him post-merging is literally an attempt to rationalize the rules so they fit around his power, rather than the other way around), then 80 levels worth of stat increases and epic feats (plus bonus feats from giving up 2 rogue special abilities) is just enough to push all his stats to 25 (the max in PS:T).
BAB, Saves, Skill Points, and HP: Once he hits epic levels, the BAB and saves don't matter (as they are replaced by the epic progressions). Still, these 4 factors differ depending on which class TNO is given first (after that it really doesn't matter). I decided to use Fighter as the 1st class (and take it all the way to the end before starting the others) because in PS:T, TNO keeps the THAC0 and number of attacks of his best class regardless of what class he is at the moment (and the only way to make that work here is if Fighter is his 1st class, since epic attack progressions do not give extra attacks). Besides, our TNO starts as a Fighter.
Eidetic Spellcaster: I never see TTO with a spellbook. Do you? And it feels more right this way for a being that might as well be a Power.
Spell Resistance: This is 3.5's equivalent to the Magic Resistance in PS:T.
Resistances: Check TTO's stats. He has a bucketload of them. Again, the specific numbers themselves shouldn't be considered important, but the trends should. Lots of resistance to some forms of damage, and a significant amount to others.
Memories of Life: I could point to what I said previously about D&D's levelling system not being ideal for describing TNO's power gain post-merging, but in all honesty, I just did it this way to make the skills easier to build and read (do you really want a half-dozen conditional skill bonuses listed there? It's already too long!).
No Fate: The fortune teller says TNO has no predefined future. And the auto-fail-on-1 and auto-pass-on-20 mechanics are absent from PS:T.
Weapons Groups and Focuses: The Weapon Group variant rule allows 3.5 to simulate TNO's inability to use certain weapons (note the lack of Heavy Blades). The Weapon Focus feats simulate the proficiencies TNO could get in each weapon group in PS:T.
Languages: We know he knows Common, Uyo, and Rebus. He must have known Githzerai to have made the Unbroken Circle of Zerthimon. And if he doesn't know Infernal and Abyssal already (he's implied to have had dealings with both Baatezu and Tanar'ri), it's a safe bet he'll pick them up after a few centuries fighting in the Blood War.
Other Feats: Scribe Scroll is a prerequisite for Etch Rune, and Etch Rune is a perfect way to simulate dormant spells that have been left around by some of TNO's previous incarnations (such as the Paranoid Incarnation's trap in the Private Sensorium). Craft Wondrous Item allows for the creation of the item that leads to Ravel's Maze. As for Craft Magic Weapons and Armor, one of those incarnations had to have turned that severed arm into a magic weapon. Eschew Materials and Ignore Material Components are there because we never see TNO using spell components. Quick Draw is to simulate TNO's ability to switch weapons instantly. Power Attack is a no-brainer. Able Learner makes building the skills easier. Endurance is a prerequisite for Hibernate, and Hibernate simulates TNO's ability to recover from lots of damage (and the strength penalties of Shadows, which would be considered ability damage in 3.5) by sleeping for 8 hours.
Fast Healing: Regeneration doesn't quite work for TNO because it converts all but specific damage types to non-lethal damage. Normal Fast Healing doesn't work because it doesn't allow one to regenerate or re-attach lost body parts. So, a special version was required. Also, 15 health gain per second is equal to the 2.5 health gain per second TNO could reach in PS:T.
+1 Heavy Mace: The weapon TNO picks up at the end appears to be a heavy mace. It must have been magical (otherwise it would have been useless in the Blood War, as so many fiends in PS:T are immune to non-magical weapons), but at the same time it couldn't have been so powerful that it would just be lying around. So, +1 it is.
Skills: There were a lot of ways I could have divided up those 929 skill points (one went to learning Uyo), but none that would have been perfectly even. So, I eventually went "screw it" and put 25 ranks into whatever skills I felt would have been at all relevant to TNO's many lifetimes, and then put 6 ranks in the others. I arbitrarily assumed that TNO had no ranks in any perform skills, because due to the vague nature of the skill, I could only put ranks in them if I specifically decided which types of performances TNO had trained himself in during his many lifetimes (and we are given no such information). The craft and profession skills would have gotten the same treatment, except we know from the game that TNO has built weapons, traps, and a tomb (and the Good Incarnation claims to have spent time as a Cartographer).
Deceased: This is a really interesting one. Ordinarily, when a mortal being dies they become a petitioner of whatever plane they end up in, losing all memories and powers. TNO is clearly not a petitioner, but is also clearly dead. We know what ghosts and other spectral entities look like in PS:T, and he's not one of those either. He also can't be a corporeal undead, because they don't remember who they once were (and TNO appears to, judging by his lack of confusion, his memory of Ravel's question, and his conviction as he joins the Blood War). He appears to literally be the soul of his dead self, so that's what I made him. He gets to be immune to Ability Drain because that specifically targets living creatures. Massive Damage doesn't exist in PS:T, so he gets immunity to that as well. The embalming spells in PS:T are effectively inflict spells that can't be used on living things (they heal undead), and they can be used on TNO, so he's healed by positive and negative energy.
Former Player Character: NPCs don't get the full HP at first level, but TNO was a player character, and his stats shouldn't change simply because he becomes an NPC.
