I have almost 100% male-paragon save-game of ME2 (imported ME1).
I also did the choices in the last mission as mentioned above and I lost the Scientist.
I`m now on my second playthrough we`ll see what will now happen.
Any chance of a save-game file upload?
p/s:IMHO, 14 hrs is kinda fast for an RPG. Took me 50+ for DAO, and i don't think this one will finish just as fast either...