Changed the battery and it set off the alarm. it seams like it activated a kill switch of some kind. is there a way to reset it?

there is no override. Otherwise it would defeat the point of an immobilizer. I would find out why the alarm went off and deal with the rot cause rather than trying to bypass something made to be un-bypassable.

You may be able to reset the alarm by unplugging the battery from the car for a minute or 2 but I would start with the alarm manual to be safe. Possibly even remote the alarm and put the wiring back to stock.

HAD TO TAKE MY FREINDS TO DEALER TO RESET THE DANG THING

Just because the lights go on does not always mean that the battery has enough power to engage the starter. The clicking noise could be the voltage regulator clicking. And since you disconnected the battery maybe there is not a great connection at the terminals. Were the terminals cleaned before the battery was reconnected?
Curious ... what was the cause of the check engine light going on?

try disconnecting the battery this should reset the system

entertain the possibility that a previous owner got tired of the alarm going off and disabled it.
if there is a question on this board almost as common as i lost my owner's manual, it is how do i shut off this annoying alarm which goes off constantly killing my battery and annoying the whole neighborhood.

There is NO kill switch on the 2000 Elantra... HOWEVER, there is a thing called the Key Fob (keyless remote entry system). There is, however, a system in place called the 'starter kill' circuit and it is activated when the burglar alarm goes off.... it's called the burglar alarm relay and it is activated to prevent the engine starter system from being used. There are three ways to get the engine started in such a circumstance... 1. use the key fob to 'disarm' the system... 2. put the key in the ignition and turn it to the 'RUN" position and wait until the alarm stops (horn stops beeping and the parking lights stop flashing), then the engine will start.... 3. pull the starter relay from the UnderHood junction box and bypass the starter circuit (key in ignition and in the 'RUN' position), jumper the starter solenoid circuit to energize the solenoid to start cranking the engine -- it should start then.

some alarms have kill switches, but most of them prevent the car from even starting. i would consider strongly getting the remote for the alarm or Completely disconnect the alarm module.

Sometimes the alarm thinks the pos. battery cable has been cut so it kills the ighition. You will have to look in the manual to see how to reset the alarm. You may need a code. If its not the alarm, you may have blown a fuse or worse, fried the computer when you put the alt. in. start at the begining. Check the battery cable connections, battery voltage, alt. wires and connections. if the headlighys work but the car won't start, it's prob. not a "connection" problem.

Removing the battery cable is something the alarm companies no the theifs can do. Find the valet button, this along with a few steps that you can find with your alarm manual will reset the system.

This is a Direct Fault Caused by the Alarm System Starter Kill. Do you have an Alarm Override Switch???? You may need the Dealership to Reset the Alarm if not.