Holy crap, I cannot believe I won with this ship!
Slimeball VI, a Slug A, was not very well armed, finishing with a Dual Shot Laser Mk II, Heavy Scatter Laser Mk II, Hull Smasher Laser Mk I, and (Oni Missile/Auto Laser Mk II). Drones were Antiship Missile Mk I & Defense Mk I. Augs were Targeting Jammer and Slug Repair Gel.
Ship stats: Power L22, Shields L6, Engines L5, Weapons L7, Drone Ctrl L3, Cloak L2, Teleporter L2 - actually everything else L2. I had a full crew to start the final battle: Engi x2, Slug x3, Human x1, Rock x1, Mantis x1.
I had a Cockatrice Missile in the mid-game, but sold it for the Oni, not having a lot of missiles and thinking the 2-damage cloaked ones would be better than three 1-dmg ones. I was not thrilled to get the Auto Laser Mk II, as it needs 3 power, and I really needed more shots. But I kept it, as I wasn't having much luck in stores. Thought about passing up the missile drone, but man, did I really need it - there were times when it was the only thing doing damage!
I had to run from a lot of battles (only defeated 26 ships), as my puny missiles might not always take down enough shields - also couldn't always afford the ammo. I didn't board till late in the game, making early use of (mostly) one of the beginning Light Lasers Mk I. Then I was boarding with squishy humans. New crew was either Human or Engi. I was in a quarantine sector and answered a lot of distress calls. I lost one of my slugs, but it was just security/damage control. I did lose a 1* shields officer, but gained a Rock Dr. Jones. Got the Mantis in sector 7.
Being low on missiles, I hit two repair stations in sector 8. Having used some in a fight, I'm not even sure I had ten when I got to the boss. I only used one boarding team, Mantis & Rock. I suppose I could have used the Human who was the B team and taken a Slug off weapons, but I didn't - I think I was busy repairing artillery damage. I wasn't sure if I was going to board the Burst Ion and Beam, but it was such slow going inflicting damage, that I did.
Round 2 was such a long battle, I thought for sure I wasn't going to make it. I could board the weapons rooms, but not the main body, as most of the boss' crew was still there. I had to use my few missiles on the shields, so my other weapons might have the slightest chance of doing damage - I only had four shots, and every one needed to count. I had my missile drone going, only to realize that the boss' defense drone was shooting its missiles down. Shit! I'm fucked! But I realized it was a Defense Mk II (or something like it), as it was also shooting my laser shots. So I'd wait till the sloooowwwww drone was about to shoot, and launch a volley of laser shots, hoping to distract the drone - and it worked, some of the time! Meanwhile I was juggling missile and defense drone, which shot down a few boarding drones, but let three through. I fought those off, but the drones were whittling my hull away. In desperation I decided to board anyway, to see what damage I could do - while keeping the missile drone active. The A team went into sensors, then the B team into drone control, followed by the A team. I had run out of missiles for my Oni, so my missile drone was my only hope. I think my boarders got hit a couple times. The second time, a fire started in the drone control room. Well, I finally pulled them back. I had pretty good timing using my cloak, but my hull still got taken down to the red. When I finally finished off the 2nd stage, I had 2 HP left!
Unfortunately, my Mantis didn't make it back, having died in the fire/melee.
So the Human was back on the A team.
That round had taken place at a repair station, so I waited instead of jumping, and got repaired. Phew! But they had no more missiles to give out. I must have gotten one for winning the round. But that's not enough, so out with the Oni Missile, in with the Auto Laser, 3 power and all. Having waited, I now had to catch up with the boss. I thought because the boss went through a beacon, I wouldn't have an encounter, but I did! I jumped as soon as I could, even using my cloak to dodge, figuring it would be back in time for the first power surge.
The fight took place one jump away from the last Federation base. Crap, the boss disabled my cloak, so I'd have to tank the surges. I got the defense drone out, and it shot one or two of the missiles. Then the surge alarm came. Oh, shit! Wait! I can cloak?! So what got disabled? Oh, my teleporter, right next to the cloak on the UI. I fought off the remaining boss crew which boarded me, shot down the Zoltan Shield, repaired sensors - no boss crew left in the main body! But I couldn't get through the shields with my weapons; only the sloooooowwwwww missile drone. So I decided to jump and see if that would get my teleporter working again.
Now we were right at the base, do or die time. My teleporter was working, but drone control was out. I got the Zoltan Shield down and took out the burst missile. Retrieved them and went back to shields. Not the walk in the park it used to be, with the O2 running out. Fortunately, L2 teleporter. Still, non-Mantises take a while to damage systems. I had to retrieve and jump back a few times. The first time the Zoltan Shield regenerated, my boarders were on my ship. The second time, they were in the boss' shield room, so after taking it all the way out, they perished. But once I took down the Zoltan Shield, that was all she wrote. I finished with 13 HP, and most crew hired at 19 (!). Only 3967 pts, but with the sweet taste of victory.
I'm looking forward to the Advanced Edition. It might not make the game files more modable, but hopefully the few things they add will give us more options.
For some reason, the links you provided aren't working for me. 
