Well, crap, I don't even remember for sure when they were kidnapped. It seemed like it happened right after I did Legion's loyalty mission. I should have various saves to go back to but it's too bad I have to leave so many undone (not to mention waste 6-8 hours of play the last two nights). Damn... The
only one I saved was Dr Chikwas (or however it is spelled). I got to see Yeoman Chambers liquified before my very eyes. I went through and did a complete and thorough scan of every single unexplored planet before I went to the end

. So, see, here's one case where I kind of wish I had seen some spoilers so I knew not to waste all the time.
I did every ship upgrade. I thought I had read the suicide mission depended on getting those done. Just curious - what happens if you don't get all the upgrades? Do you lose squad members on the approach to the Collector base?