You'll want to retrace all your connections. I've done 3 of these conversions and never had an issue. It's easy to get the wires backwards when you're wiring things up. Make sure the wire connections are intact and no bare wires are exposed and touching.
Here's a good write up from Stu's Site
. What ever you do, DO NOT
install Resistors in line to make the turn signals flash slower. You're begging for a fire.
use the approved Electronic Flasher approved for LED tail lights. EP-26
(you can get from NAPA or Pep Boys) for 1997-2000 TJ's and GCD-TJ0106
(from Gold Coast Off Road
) for 2001 + TJ's.