riverbanks

You didn't remove the cowl and stop the mod from MCM before you removed the mod. For all purposes, the game thinks you're still wearing it. Re-enable the mod in your load list, go back to a save before you removed it, unequip the cowl, throw it away, do the proper uninstallation process on MCM, and only then disable the esp.

You escaped with Hadvar and/or wore Imperial armor through Helgen, and the game now remembers you as an Imperial in Stormcloak territory.

Depending on what else you've done in game before you tackle this quest, people know of you. They recognize you, talk about you. There goes That Guy. By the time you get to Windhelm, you're at the very least thane of somewhere, if not leader of a whole faction or three and dragonborn annointed. So you get to Windhelm, and Aretino is the talk of the town, even the guards know it has something to do with the Brotherhood. And you're seen entering and leaving his house at least twice. Even more suspicious if you're seen sneaking around, trying not to get caught breaking into some kid's house. Then when you kill Grellod, unless you have your stealth maxed out or use a lot of invisibility potions, Constance and at least four children witness your kill and flip out about it. They're loud, they make such a scene of the whole deal that when you leave the orphanage, anyone would've seen some kind of ruckus was going on. From then on, gossip runs wild in Riften, a city run by its shady whispers. Identifying you and knowing the details of the kill is really very easy. You weren't half as discreet about it as you think. Now how they manage to kidnap you when you're out there armed to the teeth, possibly surrounded by followers equally as armed and dangerous, that's a fun question. But they're Brotherhood for a reason, pulling stunts like this is their deal.

Did you install SKSE correctly to /Skyrim and not /Skyrim/Data? MO can't install SKSE for you because it doesn't go in the virtual data folder, it goes straight into the /Skyrim folder. That part you have to do manually. When you installed the uncapper via MO, did you sort Skyre to load after Uncapper so T3ndo's custom ini can overwrite the ini that comes with Uncapper? If not, the reason you're not getting the extra perks is because your game is not reading T3ndo's customizations. An easy way to do this so you don't have to keep watching if they're loading correctly is go into Mod Organizer/Mods/Uncapper/SKSE/Plugins/ and rename SKSE_Elys_Uncapper to something like SKSE_Elys_Uncapper_BACKUP or whatever, so the game will ignore that file and only read T3ndo's SKSE_Elys_Uncapper file. There's no command to give you X perk points to spend. To manually add the specific perks you want, type help [name of perk] sans brackets on the console, take note of the perk code number, then use player.addperk [perkcode].

The option to buy a specific Children's Bedroom from the jarl's steward is only for the five vanilla houses. For the three houses you can build with Hearthfire, all you need to do is build either the two single beds available in the greathall crafing table, or the master bedroom in the left wing. Now why you can't move Sofie - have you adopted her already, and are you married? If you have a spouse, you have to ask the spouse to move, instead of the kids, so wherever the spouse has on record as your family home is what the adoption script reads. So if you haven't adopted Sofie yet and you're married and living in a house with no kids' room (such as a Breezehome with alchemy lab, or the spouse's original house), Sofie is reading that your current official family home has no room for her. Try first asking the spouse to move to Lakeview, then once your spouse has moved there, go adopt Sofie and she should understand that she's supposed to move to Lakeview.

She's probably stuck in some state of hostility from her quest that never cleared out right and now conflicts with her spouse AI. Alva is not a marriable NPC, so you either married her via console or mods, which always makes NPCs involved in these long quest trees susceptible to bug out sooner or later, specially if they already had relationship/marriage flags set with another character. She's unstable alright, but unfortunately it was you forcing the marriage who broke her AI.

You haven't broken anything. Rolff is just one of the zillions of potential targets for a minor radiant pickpocketing job in the Thieves Guild questline, but other than that he's irrelevant. If you're not doing the Thieves Guild in this playthrough, Rolff has no use - if you are doing it and happen to roll this specific job, just tell Delvin you don't wanna do it and ask him for another target.

I'm only ever able to connect the balconies right if I build the storage room first, then immediately build the bedroom and armory, before building any outside decorations. If even that's not working for you, just disable the railing blocking your way via console (don't mark it for delete, just disable and leave it at that).

Neither is better, it just depends on who your character is. A thief/assassin would want smaller, lighter weapons that are easy to conceal or throw away in a hurry, and probably wouldn't go sneaking around lugging a heavy clunky shield on their back. A knight or soldier with formal combat instruction might prefer the sword/mace and shield style of fight, blocking, circling and waiting for an opening - or they might be more agressive and parry with two swords/a sword and a dagger. A barbarian with a simplistic "kill all the things" mind might prefer to just hack and slash at everything with two war axes (if a big two-handed battleaxe is too unwieldy). Use what feels right for your character.

You already killed Astrid, there's no unkilling her and starting over. Resetting the quest at this point would only bug your game beyond salvaging. Just go back to your last save before being abducted or when you're at the abandoned shack and kill Astrid there.

Your Whiterun housecarl will always be Lydia, no matter who the jarl is. This is true for all of them, no matter which jarls get replaced, or whether the Imperials or Stormcloaks win the war, your housecarls will always be Lydia, Argis, Calder, Iona and Jordis (+ Rayya, Valdimar and Gregor if you have Hearthfire). If you can't find Lydia at either Dragonsreach or Breezehome, bring up the console and type: prid 000A2C94 moveto player This will teleport her to you.

Don't think it's so much the ritual itself (briarhearts have their hearts cut out and replaced, witches sort of decay into hags), but that the magics involved have similar limitations/conditions/what have you. There are no male hagravens as there are no female briarhearts, so it's probably just how the magic works for either case.

Not a matter of would, but could. A good person can still make bad choices, against their own better judgement, and for all sorts of naive, misguided reasons. Sometimes your choices seem right at the time you make them, but turn out to be very wrong in retrospect. That's the whole point of Kodlak's story, a good man desperately trying to save his now wise soul from a rookie mistake he made when he didn't know any better and honestly, genuinely thought he was doing the right thing. Roleplaying a +10 lawful good paladin does not make your character fail-proof. If you want your character to be an interesting person, not just a bland avatar of black and white Good for Good's sake, he'll have to make mistakes too, despite having the best of intentions. And he'll have to live with his mistakes, as all good guys do. The game even allows for that - that's why you're given the option to regret your choice and cure yourself after all is said and done. All of that said - yeah, the Companions questline is a trainwreck of bad writing. Everything is pushed onto you, you're forced to do exactly as you're told just to be able to move the quest forward, there's zero choice or roleplaying in it. It's terrible all the way through, there's no disputing that. So, this is the mod you're looking for: http://skyrim.nexusmods.com/mods/22650/ The full version adds a lot of conversations at key points that let you show your alignment and make your intentions clearer to the other characters, gives you lots more dialogue options through vanilla conversations so you can agree or disagree with Aela, Skjor and Kodlak to whatever degree you want (from respectfully agreeing to disagree to bitching out at full force), AND most importantly... lets you complete the Companions quest without ever taking the blood. And it makes sense too, because this time you actually told the characters why you were making this or that choice, and they told you their point of view, and it wasn't just a mess of go there, do that, quest over. *dreamy sigh* Would that every guild had a mod like this to fix these godawful storylines.

Most likely one of your is mods making the NPCs more aware, because the vanilla AI at "super sneak perks" levels is ridiculous. You can be dancing naked up on the dinner table in the middle of a full packed room and shooting fireballs at the jarl, but just crouch for a second and suddenly nobody can see you. Nobody. They're staring straight at your face, and you're still undetected. Check your SkyRe settings/modules, check your mod list one by one for anything at all that modifies AI, re-read the full descriptions and readmes of your mods until you find the culprit. That's not vanilla behaviour, NPCs are dumb as doormats in this game.