Quick Question. Motor swap issue

[snopro440r]

hey every one i need a little help one the motor swap i just did. iswapped out my 2003 motor which had a cracked block and threw in a motor out of a 2000. swap went good motor fired right up. however it doesnt seem to be charging (changed altenater), and as soon as i fire truck up it says motor is at operating temp and after about 30 seconds it says motor is over heating. checked motor and it is cool. battery light is also on. are the harness a little diffrent on them. i did change the pcm and got same results. thanks