after the upper intake is removed, you will need to transfer the egr valve to the new cobra intake, you may need a new gasket, i would go ahead and get one.
first, you disconnect the 4 bolts that hold the fuel rails to the lower intake.
after those are removed, gently pull the rails upward and watch for any injector o rings that may slip out or get stuck in the old lower intake.
after the fuel rails are removed, disconnect the end of the hose that runs from the radiator to the thermostat housing. you will also need to disconnect the two lines that run from the heater core line to the heater core itself. be very careful around the heater core. disconnect the line from the metal pipe instead of from the heater core end. the barbs on the heater core are very easy to bend.
one major pain is removing the metal line that runs from the lower intake to the heater core. you will need big wrenches for that. make sure you use new teflon tape on the new lower intake.
to disconnect the fuel lines that run to the fuel rails, you will need the plastic push tools that push on the spring loaded clip release the line. a small amount of gas will leak out. it can be frustrating to remove those lines if they have not been removed in a while or it is your first time.
after that, you just unbolt all the bolts on the lower intake that screw into the block. when you are removing the lower intake from the heads and block, use a small pry bar or large flat screw driver to gently remove intake and break the gasket seal. coolant will run out of the intake and will be burned up later.
you need to make sure you remove the rubber pcv valve grommet that located at the rear of the lower intake. take that out and use a screw driver to remove the metal screen. after the screen is removed, take out the metal steel wool like filter and hose it down with brake cleaner.
i recommend putting this in with both intake out of the vehicle so you do not have to hunch of the car to see. after you put the screen back in, bend the prongs over the screen, good to go. when i put my rubber grommet back in, i used some high temp silicone (grey one) to hold it down for good (unless i really want to remove it with pliers).
clean off all of the old gasket material with a razor. i like to use the yellow high tach silicone on the front and rear rubber gasket pieces because they hold better when you are lowering the lower intake down. you just need a little bit of the high tach silicone on the gaskets that go on the heads.
you will need to remove the thermostat housing from the old lower intake and install it on your cobra. it's only 2 bolts. you will need gaskets and you should change your thermostat while it's out. take out the heater core pipe now with the large wrenches or crescent wrench while it is out of the car. install it onto your new intake so that the pipe ends are facing the rear of the lower intake.
you will now need to reconnect the fuel lines to the fuel rails. you simply push them into the fuel rails. make sure you push the hell out of them. you will hear a click when it locks. to make sure they are locked, try pulling them out as hard as you can, you should not be able to. reinstall the fuel line caps to lock it.
after you put in the new lower intake, insert the center bolts first and work your way outwards. check to see that the cork gaskets i mentioned earlier did not move out of position. when you torque the lower intake down, go back and check every bolt to see that torqueing one end didnt make the other side loose. i do not recommend a impact wrench because you should feel that each one is tight.
after that, it's a piece of cake.
-put your fuel rails back on
-bolt them down
-reconnect all the hoses
- thermostat housing hose from the radiator
- heater core pipe to the heater core hoses
- pcv valve (go ahead and install a new one $2)
-put on the gasket that goes inbetween the upper and lower intake, use a small amount of silicone to make sure it does not move.
-if your cobra intake does not come with the egr plate+throttle body, you will need to transfer that over to the new intake. (will take some time)
-if your cobra intake does not come with the vacuum splitter that connects on the underside of the lower intake, you will need to transfer that over.
-you need to make sure there is a vacuum line that runs along the intake that connects the pcv valve to the intake.
after that go ahead and put the upper intake inplace and bolt down the middle bolts. line everything up and put the front and rear bolts on, but do not forget the ground wire. torque away. connect the small fuel pressure regulator line from the intake to the regulator. connect the hose that runs from the intake to the pcv valve (this is an easily forgotten step). connect all the other hoses than came from the vacuum tree to the intake.
bolt on your old gas pedal cable to the egr plate. pull back on the cable and snap it onto the throttle linkage. check for any binding in the cable.
connect your egr valve electrical harness to the valve. install your old TP sensor onto the top of the throttle body and connect the sensor to the harness. Connect the hose from the oil fill spout to the throttle body. Connect the hoses that run from the front of the heater core pipe to the egr spacer and from the other side of the egr spacer to the back of the lower intake. Reconnect your idle air control valve harness to your IAC valve on the throttle body.
finaly reconnect your air filter to throttle body hose. use this time to check all of the clamps on the each hose to make sure they are tightened and all bolts are tightened. look around at each vacuum hose to make sure it has a home and is not hanging somewhere.
this thread is getting long
feel free to add on or tips
need help installing a upper/lower cobra intake. 
I want the warm weather!! 
