I usually don't answer my own question, but in this case I have to I guess.
I am running Minecraft pre-release 12w36a and I can confirm that you can cure infected villagers spawned from dungeon zombie spawners in survival mode.
I had a zombie spawner underneath my base that I never destroyed, I am glad I kept it. I set up a small killing device for killing the unwanted zombies, and waited for a infected villager. In my case it spawned one every 30 zombies or so.
When I got one I used a splash potion of weakness (water bottle + fermented spider eye + gunpowder). As soon as I threw it I got my golden apple in my hand, and just right-clicked the villager. At this point he started shaking.
While he was shaking, I waited around. About 5 minutes later he turned into a normal villager.
At this point I wanted to know if he would despawn, so I went exploring in my world, slept for a few days, and went to the nether a few times. When I came back he was still standing there, which was great.
I do not know if this will stay in the game. I will update the game once in a while to see if it still works in the snapshots.
For now I will work on setting up my village, I am glad I don't have to build the 1000+ block railway anymore.
I can confirm this works in 1.4.2, see the video in the question for more details.
Yes you are missing something ;)
The solution is the game mechanics:
The hopper which is leading new bottles in your brewing stand is -always- faster than the hopper leading out.
Which means, before the cleaning-hopper below hast the chance to clear the second slot, the top one has already refilled the first.
The only way to avoid this, is to build another lever or button connected to the top hopper. (if you want to use buttons, use an inverter in between)
I got this problem a few weeks ago, i hooked up the two hoppers to a single redstone-clock-system to fully automate splashpotions of harming, which works fine for me :)
Best Answer
Lava does light up blocks below. At least in 1.6 it does. I made a small room completely blocked off from light and made a lava ceiling. Above the lava is more blocks to ensure no external light is getting in.
I know that sometimes lighting gets messed up. When I see black areas that should be lit, I put a torch down and remove it. This seems to reset the lighting in that area. Maybe try that and see if it fixes it?