u may have two wires in the distributer plugs backwards

 

Try using your stock ecu and see what it does. If not are your injectors dirty, or is the #2 wire bad . Check the plugs are they gapped right or are they fouled or are they bad.

 

Ima put it like this, the car gets spark, there is fuel comin out the number 2 port and it really doesnt matter what ecu u used cuz ive used the stock one and an 88 integra piece. would a fuked up head cause this? warping? bad rotor (distributor)?

 

If the wires are bad you will still get spark but it my be weak and a weak spark will cause the cylinder to seem dead. If the injectors are dirty you will not get enough feul and the car will run bad . Yes a warped head or blown head gasket could cause. Does it smoke and if so what color. Does it have compresion on the cylinder and if so what is compresion on all for cylinders.

 

Do a compression test on all cylinders. If #2 is making good compression, start up the car. Pull out the spark plug wire from cylinder #2. If the engine sounds the same without "dropping" in power, then try replacing the spark plug wires.

And also did you do a valve adjustment after installation?

 

put the old head back on and yes cylinder two does fire

 

when you put the y8 head on did you make sure it wasn't 180 out of time. i would chech that and that seems to be your problem from what ur saying. my friend had the same problem when he put a z6 head on his. it idles fine, but ran like shit and wouldn't rev over about 5500. try that and lemme know what happens.