One issue is the Skaa vs nobility. In the book one character mentions that the nobility are the descendants of the people who sided with TLR from the start. There is some evidence supporting this. Such as TLR mention all the stuff that was done to him to try and kill him (i.e. being flayed), implying there was a struggle at the start, and he had to fight for his power and needed allies to do so.
However, at the same time, Rashek HATES the people Aendi was apart of (from Khelenim or something I believe). So it makes sense that that would become the Skaa. If they became the skaa, who became the nobles?
A lot of the diary entries are of Rashek talking about how his people should be dominate. You could almost make a case for the terrismen becoming nobles and Alendi's people becoming skaa, if there weren't the other terrismen around.
I'm not sure if the choice of which peoples became nobles and skaa is ever really explained. Rashek may well have turned Alendi's people into the skaa. The nobles were probably just carried over from any existing power structure that he didn't especially hate. Rashek ended up not raising up the Terrismen because he feared the possibility of someone else being born both an Allomancer and a Feruchemist and being able to match his abilities.
During the end Kar also mentions how in order for Vin to be as strong as she is, she had to come from a "very pure bloodline." Which bloodline is that? Aren't all nobelemen of a pure bloodline since interbreeding with skaa is so forbidden?
That would be the bloodline(s) descended specifically from the 10 or so kings and lords that Rashek gave beads of Lerasium to. As for interbreeding being forbidden, when has that ever really stopped people from doing something? Yes it will stop some, but 100% all the time? Not going to happen.
Also, with TLR being stabbed in the chest, flayed, etc (even beheaded if the stories are right) and him not dying, what is that exactly? It's similar to the Inquisitors so it could be a property of Hemalurgy, but other than the bracelets he doesn't seem to have the spikes that they do. Or is it just a super stockpile of stored 'health' from his Feruchemy that he can burn with Allomancy to instantly heal himself? Brandon does confirm in one of the annotations that TLR uses Hemalurgy, but I'm not sure to what extent. I.e. a spear through the heart killed him when he was old, so it makes sense that a spear through the heart would of killed him when he was young as well (such as when he was stabbed right before Kel's death)
One of the annotations mentions that the story about beheading was exaggerated, and that if Rashek's head actually came off it really would have killed him. Surviving wounds like that is a function of supercharged Feruchemic healing, possibly combined with burning Pewter Allomantically. As for the spear killing him at the end, I think that was really more window dressing than anything else - he was about to die from old age anyway.
Finally, I'm trying to understand exactly how TLR became immortal. When I first read the 1st book and was waiting for the 2nd and 3rd I always thought he was storing youth in the Atium and then burning it to get a larger amount of youth than normally allowed by Feruchemists, and staying young that way. However, we now know that isn't true, the Atium was somewhere else (it could of been some other metal of course).
I think after rereading carefully, my impression now is that he would go into that room of his for 3 hours or whatever it was every few days and make him self old, storing youth into his bracelets. Those bracelets then became a piece of metal with the 'power' of youth stored in them. He could then slowly burn the metal in those bracelets (without ingesting them?) over the course of the next few days and keep his youthful appearance. So in a way, he was able to 'create' a new metal to burn with Allomancy. Ideally you could do that with any of the things Feruchemists can store, and overwrite the metals Allomantic effect and have it give off a new attribute when burned. Does anyone know how accurate that is?
The giant stockpile of Atium was somewhere else, but Rashek didn't need such huge amounts of it to maintain his youth. Your initial idea was accurate, though portions of your new impression may also be correct. I think the system went something like this:
1) Store youth in typical Atium bead.
2) Ingest and burn bead with youth stored, gaining a sudden burst of a LOT more youth than he had originally stored.
3) Simultaneously store the new youth in his Atium bracelets, charging them up while preventing a sudden regression to baby-hood.
4) Gradually withdraw youth from the bracelets to maintain himself.
He'd only be doing the store/burn trick at intervals in private, and that's when his age would really fluctuate. Most of the time he'd just have a giant stockpile of youth stored in the bracelets and be drawing on that the normal Feruchemical way. The whole process would consume and use up Atium over time, but I think it would be a small enough amount to not seriously affect the main stockpile's size.
Then when he lost the bracelets, all of a sudden he went to his proper age of 1000 or so years, and his entire body started falling apart.