You know, I just had to register to these forums, just for the original post of this thread. At first, I just have to say that you guys are awesome in some really twisted way. I mean, minecart shotguns, "child care" and such. I just really hope that I would never irl have to test anything designed by you. Unless, perhaps, if you plan to make me a super soldier.
Anyway, I didn't read the whole thread, just a couple first and last pages and I just decided to give my $0.02 how to go about the "training". That is, if it works in the first place. And this is probably something someone here has thought of already anyway.
1. Carve a long entrance cavern to the fortress and a drawbridge after that and enough individual rooms for your future army between the bridge and the entrance and put a small drawbridge on each door.
2. Seal in kids with armor and training pets, using pasture, assigned beds and whatever and when the kid goes to sleep, just close the bridge.
3. When they grow, draft them to the military and issue them the armor they have in the room and a post outside the entrance.
4. When a siege comes, just raise the main drawbridge and let loose the army of super lunatics.
5. Watch the circus.
Of course butt naked super lunatics would be more entertaining but perhaps had shorter lives.
Then after the siege, just wait for them to go to sleep again and raise the bridges one by one. Rinse and repeat.