I'm using the Mindcrack Pack.
I'm trying to have a have an ignitier on for a small amount of time to set chickens on fire (just enough to kill them without burning the drops), which are then picked up by a relay on which they are standing on. I want wired so that it can be easily turned off or on. Once the lever is outputting a signal, I want it to turn on a loop, where the igniter is briefly turned on every x seconds (turns off right before they die or so). If the lever is off, I want the loop to end, without the use of noisy pistons.
Where are you getting the chickens from? If you're throwing them in there manually, you could probably do quite well with a button connected to your pistons. If you're automatically dropping chickens (from eggs in Dispensers or Deployers, say), you'll probably have better luck with a state cell triggered by whatever triggers the dropping of the chickens.
Say you want to have a chest that, when you put eggs into it, will throw the eggs into a small hole, then set any chickens that spawn there on fire, then extinguish the fire and collect the drops.
If eggs are the only thing that will ever go into the chest, the simplest thing to do would be to replace the chest with a Relay, which will automatically eject anything in it into any Pneumatic Tubes on the side with the small hole. If you want to be able to place anything else in there and not have the items get sucked out and/or have more than nine slots of storage (in case the system gets backlogged), you'd be better off with a regular chest (or an iron chest, Factorization barrel, GregTech quantum chest, etc.) with a Filter attached (make sure the side with the large hole faces the chest, and the opposite side (with the small hole) faces the tubes) and a Timer on some short delay (I forget the optimal setting, you'll have to play around with it) attached to one of the other sides of the Filter. Put some eggs in the Filter's inventory- if you put one in, it'll pull only one egg from the chest at a time; if you give it a stack, it'll pull a stack at once.
Then, run a line of Pneumatic Tubes from the output of the Relay or Filter to the input of an Item Detector. I don't remember which side is the input and which is the output, so if it doesn't work, use a Screwdriver (or Sonic Screwdriver) to flip it around. There should be an option in the Item Detector's GUI to emit a pulse for every item that passes through. You'll need to click the button in the block's interface once or twice to get to it, but I don't remember how many times exactly or what the image shown in the proper setting looks like. Place a bit of redstone on the ground next to it and run a stack of items through; the setting that makes it flicker a whole bunch for a while is the one you want.
Then, on the output of this Item Detector, place a Deployer. When you run some eggs through the Detector, it will emit a redstone pulse for each of those items. This should, in turn, trigger the Deployer once for each egg, which will then throw them. If it doesn't work, you might need to use some redstone or red alloy wire to connect one of the sides of the Item Detector that doesn't have a tube attached to the Deployer- I don't remember if the Detectors emit redstone from the faces that connect to tubes or not.
Now, you should have a contraption that takes eggs and automatically throws them to occasionally produce chickens. You'll probably want the Deployer to throw the eggs into a 1x1x1 space, with one wall or ceiling being the Deployer itself, another being an Ignitor, and the floor being a Transposer. Make sure that the large hole of the Transposer faces upward, as this is the only way that it will collect dropped items. Below it, connect some more Pneumatic Tubes that lead to wherever you want to store the drops.
As for the Ignitor... I think the most effective way to wire it to the rest of your system would be to place a State Cell set to a 1-second or so delay such that the Item Detector connects to one of its inputs, and its
second output (the one that faces away from you when you place it) connects to another State Cell, whose
first output (which faces left, initially) then is wired to your Ignitor. Each item that passes through the Detector will restart the pointer on the first State Cell, which won't do anything of importance until a second after it stops being reset. By this time, all the eggs that triggered the Detector have already been deployed. When the first state cell's timer runs out, it will briefly pulse the second cell, which will then send a longer pulse to the Ignitor, which will burn the chickens and (if you've set it correctly) turn itself off before it burns the drops. You'll need to tweak the delays on the State cells so that everything works reliably, so that the Ignitor doesn't turn on while the Deployer is still throwing eggs, and it turns off just before before the chickens burn to death.
In short: Eggs in pneumatic tubes pass through an Item Detector and into a Deployer. The Detector, for each egg, triggers the Deployer and resets a State Cell. The Deployer chucks the eggs into a small hole; once all the eggs have been deployed, the Detector stops resetting the State Cell, which then triggers another State Cell, which in turn triggers an Ignitor for a second or two, which burns the chickens, which then die and drop their feathers and cooked meat into a Transposer, which sends them into your storage system.
Can't this be done with just plain lava? Put some hoppers beneath the killing floor, the hoppers will pick up the drops before they burn, that's the way the hoppers are coded.
It's cool if you want to do it another way, but if it's giving you this much grief..
Here is an example:
This farm will either cook or drown your chickens (raw chicken for villager trading) and get you all the drops. This is vanilla. (granted it's 1.7 vanilla, but the concept is still valid for 1.6)
He said he's on Mindcrack, which, if I remember correctly, is in MC 1.4.7. No hoppers there.