1 What's at the far end of the boat trip from Lake Lucerne?
A place called Flüelen. The station is right next to the boat pier, so transfer is easy. The attraction of the trip is that the lake gets increasingly fjord-like and spectacular the further you get to the far end. The boats call at many places on the way, some also with bus or train connections, so you can do shorter trips if you want. Or just a loop back to Luzern, but then you miss the best bit at the end.
2 Will our Swiss Pass cover all those places mentioned? (Wengen, Mannlichen etc..etc) real life exp.
As far as Wengen, but no higher. See the official map of what is covered here: https://www.sbb.ch/content/dam/sbb/de/infotexte/uebersichtskarte-sts.pdf.download.pdf
4 Is it still lush and green in October? What kind of weather are we trying to avoid here?
Yes, but there might be a few snow flurries if you go very high.
5 Can 1&2 as stated by Chris be consolidated into 1 day?
Pilatus or Rigi yes, Titlis no, it is a bit further and not on the lake.
For Pilatus or Rigi, you can get a boat to the mountain, up one side, down the other and a train back.
Pilatus, see here: https://www.pilatus.ch/en/discover/golden-round-trip/
Rigi here: https://www.rigi.ch/en/Experience-Enjoy/Summer/Summer-experiences/Majestic-Round-Trip
or here (alternative route): https://www.rigi.ch/en/Experience-Enjoy/Summer/Summer-experiences/Classic-Rigi-Round-Trip