So I just did something that I didn't even think was possible: Beat the final boss with only 2 crew members.
At this point I've become so proficient at FTL that it typically doesn't hold my interest as a lone activity, but as something I do while doing something else which also doesn't hold my interest as a lone activity (such as talking on the phone). Don't get me wrong, I like talking on the phone, and I like playing FTL, but neither of them alone really uses my full brain power for the most part, so I start getting incredibly bored unless I'm doing them both simultaneously.
In Sector 7 or so, I started getting into a deep part of the conversation during some major ship fire + boarding attack, and lost 2 of my important crew members (a Zoltan and a Human). Unfortunately the human was my level 2 weapons guy (OUCH), and the Zoltan was my engine guy (bye free energy). After the battle ended, I considered restarting the game because I knew it wasn't possible to win with just 2 crew members, even if my Stealth Ship was pretty tricked out with weapons and gear.
My weapons (probably the best setup I've had so far against the boss [well it would have to be to win with 2 crew members]) were an MK3 Burst Laser, a Small Bomb, and a Lance Beam. At the beginning of the battle I would cloak my ship (Level 2 - so 10 seconds), then when that ended, I put the Bomb into the Shield Bay. After Bomb exploded, I would hit the Shield Bay with my 5 Burst Lasers. Then I would Lance the ship, making sure to hit the shields in the process. I also had a nice Beam Drone making chopped sushi with the enemy ship once the shields went down. Against the boss it typically took two volleys to get the shields permanently down (so that my Beam Drone could go to work), then after that I just ripped him to shreds.
After the second phase of the boss fight, I got extremely lucky and found a second Engi as part of a random scenario, on the way to a healing station before the last fight. I'm not sure I could have won the last fight without that 2nd Engi, and without some luck in terms of not losing the wrong subsystems at the wrong time.