Paul - The Inner C's and Center Section of the JK are cast steel not cast iron, so no preheating is required. You just want to allow it to cool slowly and if you have one put a welding blanket over it after welding.
You can leave the axle in the truck during the installation, just make sure you can drop the axle as far from the frame as possible to allow ample room to do proper welds on all surfaces. Most shops put the Jeep on a lift and take off bottom shock bolts and disconnect swaybar and let the axle swag.
The Balljoints should be swapped after welding inner C gussets.