2002 neon keyless entry problem

OK so the wifes remote quit working the other day. I replaced the batteries in it and it still did nothing. Searched the threads on here and tried the "Hold the lock and unlock buttons for 7seconds " fix to no avail. Is this a PCM issue? I also am having problems with it shifting could it all be traced back to a problem with the PCM and it malfunctioning be the whole issue? Does it control everything or does it have a body control module like some GM cars? Sorry for all the questions but I am a GM guy and I am a little lost on Chrysler products........:frown:

Open the remote up again and make sure you have the batteries facing the right way. You can use either 2 stacked CR2016s, or 1 - CR2032.

The batteries are the correct ones and in the correct way....... and I know the car sort of recognizes the remotes because when you do the hold button learning the car does chime. Fuse for the RKE system is good and batteries in both remotes are good..... and both remotes make the car "chime"

If you have at least 1 working remote, you can try these instructions:

Press (LOCK) button 5 times at 2 second intervals to resynchronize transmitter. Attempt to function transmitter, if working as designed discontinue programming.
Turn ignition to run position. (Allow ignition chimes[UNLOCK] to stop).
Using any original (working) transmitter, press the [UNLOCK] button for 4 to 10 seconds.
Within the specified 4 to 10 seconds, continue pressing the [UNLOCK] button and press the [PANIC] button for 1 second and release both buttons. A chime will sound to indicate that the transmitter programming mode has been entered (allow 3 seconds for chime to sound).
Press [LOCK] and [UNLOCK] buttons simultaneously for 1 second and release.

Press and release any button on the same transmitter and a chime will sound after successfully programming the transmitter

Repeat steps 5 through 6 to program additional transmitters.
Turn ignition to OFF position. Transmitter programming mode will discontinue after 60 seconds. (All transmitter programming must be completed within time specified).