The Ignition and autostart

The act of replacing the battery will not damage or effect Remote start up or ECM functions. Either this is a coincidence or when the Battery was replaced you inadvertently affected a ground strap. Ground straps are placed against painted panels. These panels can arc because of poor contact surface area. A poor ground will affect different on-board systems. Please start there. The autostart feature utilizes the same circuits that the ignition key uses to start the vehicle. The only difference is the autostart system bypasses the anti theft circuit at the ignition switch. If you can duplicate the symptoms consistently and are sure the autostart system is affecting ignition operations. These issues would go back to the PCM. Ignition voltage could be affected by a short or faulty component. The trouble code is a misfire code to cylinder number three.

you will need to check all you fuses on the car its self and for the remote start system. also there is usually a switch to turn off the start function. the switch could be off or bad also. hope these few tips help. you could also have a loose wire to the starter or the relay could have went too. good luck.

Your Jeep should have a "chipped" ignition key. If it does, then the programming message is telling you to insert a NEW key which has not been programmed. Somehow your jeep confused itself into thinking this way. This sometimes happens when physically inserting the key too quickly into the ignition switch after using the remote start function/ feature. If you are in a bind, you can try disconnecting your car battery and leave it unplugged for 10+ minutes. Then reconnect it and try to start your vehicle. If that does not work then maybe it is possible to obtain another NEW "SENTRY KEY" and have your your jeep program it to possibly quit the no start program loop. If these options do not work for you, then unfortunately the vehicles computer module will have to be "flashed" and troubleshooted at the dealer.

Replace the ignition switch

clicking when you turn the ignition on most vehicles could be one of two things. First the selenoid for the starter. Second the batterry is worn out or drained. Since your jeep starts with the remote its not your battery. Lucky for you your remote starter is like having a second selenoid. If you are so inclined you might try to fix it yourself. Open the hood. Have someone else turn the key. Follow the sound. I don't have a jeep of that model to look at but It could possibly be comming from a two post terminal that is realatively easy to change. If you are worried about reassembly take pictures before you start. Clean all connections that look corroded.

check your brake switch. if high resistence it can cause override for autostart.

put your key into the ignition switch leave it in the off position, press remote start, if it starts then the transponder loop needs adjusting or the bypass modual may have become unplugged

you have a bad key or transponder in the ignition. depending on what style senty lock by pass they used when installing remote start and if i knew that it would help me diagnose it but if it is a 1994 then there is not to many options so i would have to say you have an issue with the key.

Curious, do you have an autostart installed? I had that happen that the Autostart shorted and just kept telling my starter to continue cranking

You can't disable it, you have to buy a bypass modual to bypass it during remote start, the wires are in the ignition harness I have them in stock if you need one