A small suggestion for the confinement rooms, if you can spare the space.
Build cisterns above the cells and sewer corridors running under them. In each cell, place a lever-operated hatch cover in one corner, naturally this hatch should be made out of very valuable material, masterwork, encrusted and etc. Directly under each hatch cover should be an upwards ramp, and directly to the side (or sides) of the ramp should be a wall grate or floor grate which connects to a drainage pipe (directly to the caverns or an aquifer level if you happen to be above them, edge-of-map drainage will drain too slowly to avoid mishaps). To the ramped tile, build sealed access tunnels which you can open at your discretion.
Periodically open the hatch and dump the cistern to wash all rotting corpses and test subjects into the 1x1 ramp, making sure to avoid doing this during tantrums (you wouldn't want the test subject breaking up your grates and escaping). Close the hatch after the test subject and a majority of animals climb back into the cell, then send your hauling dwarfs to cart away the dead animals and re-pit and/or reassign any live ones (don't forget to check if the food stockpiles got washed away and need restocking). With this system, if a surfeit of aggressive animals begins to cause sleep-deprivation it can be whittled down, miasma-producing "accidents" can be disposed of, and as an added bonus the primary subject should also receive valuable swimming lessons from this process.
I'd also suggest that the feeding/pitting access have a shaft at least 10z high, designed so that food and test animals may be pitted in from the level directly above the pits, while prisoners, livestock and etc. may be regularly pitted from the highest level into any cell you feel hasn't seen quite enough horrifying deaths. Expendable friends of the test subjects should also take the high drop, at carefully spaced intervals. The occasional live wild animal (the size of, perhaps, a fox or badger) could also be pitted via the short drop, to allow the test subject a more prolonged training session in biting, kicking and striking skills)
And finally, I have to find some directions to this "baptism by fire" concept so I can try it out. It would strike me as being wiser to burn the supersoldiers first, since I'm guessing it's a shorter and more dangerous process, before investing 12 years and countless turkeys, fort resources and hours of personal oversight into their upbringing in the conditioning cells.