1. If a quest is unfinished, the game just reads it as started, but not done. If it is broken, it is stuck with the game thinking that. So they won't just disappear from the quest list.
2. I'm assuming you mean how she is in the marriage faction, but not "in" the marriage faction? They haven't said anything on it yet, although it seems like an easy fix.
2 Notes: The time between a patch going on Steam to then it goes on consoles is only about a week. They likely don't get too much communication, just a notification when it is improved. But it isn't too long of a wait.
3. Items with the same name have been notorious for not stacking since at LEAST Oblivion. Not much you can do there. And as it is a quest item, you can't drop or store it either. Why you aren't allowed to put them down in a player owned cell or chest is beyond me, but that's just how it goes.
Personal Opinion: How can you just be about done with Skyrim? Is that Nord your only character, or have you made thieve's, mages, assassins, and other things as well?
1. Too bad... I like to see a clean slate of what's still open to do and ignore the broken or finished quest list below the line.
2. Yes, I mean in the software bug sense--not the STDs sense.

3. Why can't/won't Bethesda fix this?

I'm not about done but I'm tiring out on some things. I've played it about daily for several weeks now and may have several weeks still to go and so far it has amounted to ~216 gaming hours. The Nord is my only character and there is nothing driving me to play any other characters. I've reached the point now that I only pick up 'meaningful' items and still have so much stuff to sell stored in the Whiterun house where Lydia just sits now. The problem there is that the shops there don't carry enough gold and right now I'm not needing anything I can't find searching through the dungeons, etc., that I pick up for free. I review items all the time and seldom see something I could pick up better then what I've got. If it is green the chances are it isn't equipped or it doesn't have any magic associated with it and isn't far off damage wise. So far many baddies can go down with one poisoned hit from the battleaxe.
P.S., When many battles get heated the NPCs get decapitated and you can watch the heads roll around like a bowling ball. I once chased an apple rolling down a trail to see just what would stop it. Fun with physics. Not so fun...or not fun at all is getting stuck in the rocks some where. I have saved over ~850 times but delete all the old saved games down to just the last few.
Also of little fun is crouching to get under something thinking that that will make a difference or stepping over a board that blocks your path. Crouching to get under something is a very interesting programming problem that the industry should address next. If you come up to a structure that is clear underneath and you crouch and can see your way through it makes no difference. Or if you get stuck in some space with your head and you crouch you should be able to crawl out and away from the obstruction. In either case crouching makes a difference with the graphics view but makes no difference at all with the physics involved.