the best thing i found to do was to put axle and frame on separate jack stands, frame at ride height, axle at full bump. full bump is typically your worst case scenario for a lot of components.
with the steering hooked up up can move the axle forward until there are issues with steering. once you are happy with the stretch and full bump drop in your links or make some mock up ones to check for clearances to exhaust, drive shaft, etc... if everything clears now you can bolt on some tires and check lock to lock. its also good to articulate the suspension and check lock to lock. you will find rubbing issues in the cherokee's notoriously small wheel wells depending on tire size.
this is also a good time to adjust your bump stops and limit the suspension for droop. steering, shocks, suspension geometry, and drive shaft operating angle can effect your droop numbers. if you are moving the coil buckets, a plumb bob off of the spring tower will help show you where the new ones go. position them after checking full bump, ride height, and full droop. i like my coils to be happy at ride height, but my bump stop striking square at full bump. there isnt as much load on the spring on droop, so as the suspension arcs rearward, i dont give as much priority on that (in a rock crawler).