Number one question.. pinion nut torque - Before loosening the pinion nut, take an inch pound torque wrench and check how many inch pounds it takes to turn the pinion over. Reason being you do not know who set up the rear end or their spec. Write the number down. Now remove the pinion nut and replace the seal. Install the nut and torque it to around 90 foot pounds. Check how many inch pounds it takes to turn over the rear end. Torque more if the number is low.... When installing a new sleeve behind the flange, the torque needed to find the right inch pound spec may be up to 200 foot pounds of nut torque to set the sleeve. I recommend you have someone help you that has experience doing this if you have never set up a rear end before... hypoid gears take a finesse to set up proper and not have issues later on.
Number 2 question.. those caps - They are threaded and not grooved as you are thinking. You don't just turn one in and not the other unless you are initially setting up a gear set. Don't mess with them if you have no experience at setting up hypoid gear a rear end. Once the procedure I mentioned above for installing a new sleeve has been completed and pinion depth set, those covers are turned in or out while using gear paint to set the tooth contact pattern. The bearing cap bolts must be loosened in order for the caps to turn. By turning them it moves the ring gear closer or away from the pinion. You don't just turn one in and not the other unless you are initially setting up a gear set. In relation, this will show on the contact pattern of the heal or toe of each gear tooth and where the pinion gear teeth contact the ring gear. If the ring gear is moved too far away from the pinion and the rear end put under load, it will rip the teeth off the ring gear. On the the hand if the ring gear is moved too close to the pinion it will cause heat and drag which will burn up bearings and gears. Do not attempt to "set the caps in a different groove" as you said because you will wind up buying a new gear set in the end.
Find someone who KNOWS how to set up a hypoid gear of this size and have them show you how to set gear tooth patterns with paint plus set up a dial indicator to set the backlash properly. If you feel daring and have time and money to waste, search for how to do it on youtube LMAO (I don't suggest this) Replace your seal like I mentioned in the first paragraph or find someone who has experience ant the right tools and gauges to properly set up the gear and have them school ya by the hands on technique.... it's the only way to fly
~Gimpster~