1) only the generic blow up the brain ending, but more then one type of craft can get there now.
2) Probably some specifics set pieces and arcs are largely missing, but there has been a ton of new stuff in the last 8 months.
3) There are a ton of guide pedia pages and most are pretty detailed, downside is that the engine level requirements for a pedia entry, requires it to be a tech all its own. So there are now somewhere upwards of a 100 of the things. And they are mostly linked to research of captives. Its nicely organic from a fluff standpoint, you learn things as the gals do, but its pretty annoying from a player technical standpoint. But that said if you want to read everything in one swoop quick battle has all techs unlocked so you can goo look at all of them if you really want.
4)The link on the first page is the complete package, aside from the original UFO files required to run any opencom mod. There are a few submods floating around but those are are mostly just QoL alterations. Or in the case of greattuna's piloted tanks and ACs in the process of being integrated into the main mod.