EDITED: After a bit of clarification in the comment, and a quick test, a slightly modified answer.
On your second play-through in "New Game Plus" mode, once you get to the point where it says you won't be able to go back, it will act like the first playthrough, in that you have to continue through to end the game. However, when you are finished with the game and after rolling the credits, you can Continue your story from the main menu. It will take you back to the Bastion before you entered the final zone. So, 1. The game dumps me in the Bastion right before I entered the zone, allowing me to play through the other areas some more. is the answer you're looking for.
DISCLAIMER: On my New Game Plus, I chose "Evacuation" as the end game choice. I do not know if this has any bearing on being able to continue or not.
That being said, you can do really go either route:
- Beat the game, and you then continue and beat the Vigils, or
- You can not beat the game, and complete any remaining Vigils to get that achievement, complete the Who Knows Where areas as you mentioned, do anything else, then when you're ready, complete the game to finish it off and get the last achievements.
If you're looking for a suggestion, I would go with #2, complete any other achievements you need to, and then finish up and make the other choice that you didn't make in the first playthrough which will net you with another achievement.
One thing I am unsure on is whether or not when you continue the Story after beating the game is if any experience you earned in the final zone carries over with you. I did not track this.
I have this issue too, but for me it's also picking up the resolution of my main monitor and using that, but displaying on the second monitor! I have a 27" 2560x1440 and a 24" 1360x768 monitor. The combination was driving me nuts as I can't even use the menu to do the workaround posted by Oak.
My solution after reading the forum post linked in the question was to add -windowed -noborder to the startup options in Steam, then it runs in fullscreen windowed mode from startup and loads in the correct place on the correct monitor at the correct resolution. It also seems to be the only way to get this particular mode active, which is fine for me as it's my preferred way of playing games.
Best Answer
There's no use for them, and there's no way to dispose of them. Fortunately, you really never have a reason to go into your backpack (unless you like flavor text), so the only reminder of the fact that you have way too many upgrade items is the counts you see beside each weapon when you visit the Forge.