As its running now... doesn't matter
The JK uses Cam and Crank sensors to figure out what's going on, the crank ( flywheel / Drive Plate ) is used for RPM and to measure cylinder to cylinder acceleration variations ( ever wonder how it figures out it has a misfire - now you know ) whilst the Cam sensor is used to determine what phase ( suck, squeeze, bang, blow ) each cylinder is in.
The flywheel / drive plate "windows" aren't symmetrical, which is used as sort of a "missing tooth" sync system..... the exact position doesn't matter...
Anyway....... anythings better than pulling it the box out again