I have an 03 TB.I changed my fan clutch,when i reset my battery the TB will only start with the remote,when i use the key,all the lights etc. work but wont start

Welcome to AF. This is not a factory remote start, correct? Also does the security lite on the dash stay on when it will not start?

re programm it as when the battery was unhooked the bcm lost its memory of the key to the switch. reprogram it as the owners manual states. it should be as before once it is reprogrammed.