Bug: Selecting E when prompted doesn't work

[Parnassus]

I ran into a separate bug last night (With Our Powers Combined/Defend the Castle [against the BoS] never started) and had to use a console command (setstage 000dfb3c 580) to move past it. Since then, I've run into two core issues that I can't find others posting about.

1. When selecting a quest, the map marker for it never appears (example: Weathervane: Broken Monorail)
2. I was able to locate where to place the MILA for the mission without a map marker, but when prompted to place the MILA on the platform by selecting "E", the action cannot complete. It continues to prompt me to click "E", but clicking "E" doesn't work and the quest can't be completed.

I have a terrible suspicion that I messed up something when entering the console command, because neither of these issues have happened before. Does anyone know how to straighten out these issues?

Note: I don't have any saves prior to when running into the Defend the Castle bug, so I can't "start over" or anything (unless you know a magic trick I don't).

[Pvt. Stash]

For item 2 I have an issue where it doesn't accept E but it accepts my Enter key.

No help for item 1. Sorry. :(