pilot bearing can stay...you have the option of pulling the seal with main cap in place using a screw and pliers, and then pounding a new seal in square using a piece of 4" abs and a coupling...(search for rear main seal tools...) I prefer to get a pan gasket and do that "while I'm there".the procedure is to drop the pan, pull the rear main cap= 4 bolts total-don't drop it BE CAREFUL with the bearing, set aside and simply grasp the seal with the fingers of one hand and pull it out, clean seal surface gently, replace seal with lightly lubed lip and a slight twisting motion as it finds its seat. lube bearing face and place permatex #2 at the edges of the main cap...(search for how not to build 2F for pic of where...pg 7 I think...) torque main bearing cap in place at 85ft#, clean pan sealing surfaces and install new one piece pan gasket. you can take the opportunity to flip the gears in the oil pump and check the rod bearings if youd like, while you're there. don't forget to use a sealant on the flywheel bolts- I used a liberal amount of loctite blue this time, torqued the wheel to 64 ft#. if your pilot bearing is good and you don't have a new one in a new clutch kit, then run what's there, otherwise, while you're there...it's got to be the hardest place to get at so no sense in leaving things that may cause irritations later; same for the throw-out bearing...don't forget to have the flywheel surfaced, too...dang rabbit hole, huh?