I've reached near the end of the quest and it tells me to continue helping Father. I've done mass fusion and mankind re-whatever and the only thing left is end of the line and that burns your bridge with the railroad. Is there something I'm missing or haven't done? Or is it as I fear and I'm hosed? I did a couple of the repeatable institute quests but nothing changed.

You are at the end of the game not sure why you think you are hosed unless you didn't want to side with the Institute but the game is pretty clear before you start the Mass Fusion quest that there is no turning back at that point.

I can't get underground undercover quest to finish for the trophy. It keeps telling me to keep working with Father as the next step in the quest, but the only I can do for Father is kill the Railroad which makes me fail Underground Undercover. Some guy supposedly shows up to advance the quest but he won't appear so I think I'm in trouble.

Have you spoken to the guy in the institute you meet in a store room?

Yes, I gave him weapons and killed some guards for him

Yeah I think you have gone to far if you have been the the mass fusion building but it should have auto failed all the faction quests. Since it didn't I don't know but I seem to remember that guy didn't want to talk to me once it became known I was next up for the directors chair.

It's weird I was done with Powering up and Desdemona still talked to me and sent me to meet the Patriot. I guess I'll load an old save if I cannot find a solution

You have to do the bit where the Brotherhood attacks the Railroad, Precipice of War.

Cool, once I get home I will check that out. I warned Desdemona of the threat from the Institute so I guess I need to figure out how to start precipice of war.