This happened to me once when I replaced a battery in my 1993 Grand Cherokee. I think all I had to do was disable the security with the keyfob. Close all of the doors and lock the vehicle with the remote then unlock it. This should turn off the security system. You should then be able to start the jeep without it stopping after a few seconds.
Welcome to the forum. Hope this is you biggest problem.
2000 Jeep Grand Cherokee V8 Stock
93 YJ I6 hard top (really belongs to SPEED)
RE 4.5" Extreme Duty Lift, Advanced Adapters SYE, Tom Woods CV Drive Shaft, EA589 10" rims with 33" x 12.5" MT/Rs
Bullet Proof Front and Rear Bumpers and Tow bar