Just easier to list my bugs to hope anyone else has found a fix for these.

1. Bring a Dragon Scale and a Dragon Bone to Esbern.
Did this, he gave me the potion. Drank it, nothing happened and the quest is not finished.
From UESPWiki:Skyrim:Esbern

• The miscellaneous quest callen "Bring a Dragon Scale and a Dragon Bone to Esbern" is bugged too. After giving him the scale/bone, he will give you a potion called 'Esbern's Potion' that is supposed to give you a Dragon Infusion perk. Unfortunately, it doesn't and the quest doesn't disappear from your Journal either.

2. Investigate the Boethiah cultist.
Killed some dude, went to check out the cult. Finished the Quest line and now, this quest is unfinishable.

3. Help Selveni Nethri escape the cave.
Ran out the cave, but like usual, I Whirlwind Sprinted out the cave, just something I do. This caused her not to exit the cave, and after going in she was past the point where it would trigger her to exit the cave. Killed her thinking it would remove the quest from my log as failed or something. Nothing. Still wants me to help a dead woman escape from a cave.

4. Find the source of power in Silverdrift Lair.
Received the letter from a friend, but instead of saying the last place I've cleared out, it said I caused a stir at Silverdrift Lair (Never been in there before) and told me to go search for the source of power. Went in, cleared it out, and the wall with the words on just makes the noise as if I'm collecting the word, but the screen doesn't "blackout", the word doesn't light up or do any effects and I cannot get the word. I checked UESPWiki and apparently I already have the word of power.
From UESPWiki:Skyrim

• After you learn the "disarm" mark, there is another door you must unlock to exit the lair.

This game is an amazing game and I love it and will continue to play it. I probably will start again but so far with over 100 hours on this guy, I might as well finish him up as much as I can before starting someone new.
Just let me know if you've had any of these problems too or if you've found ways around them.

WhoGotTheChunk