Since the Tracker does not have timing marks on the edge of the flywheel like the Samurai, I would not worry about any indexing of the flywheel if there is no factory indexing. If you look at one or both sides of the flywheel, you'll notice holes drilled part-way into it's surface on unfinished locations. These were drilled during the balancing process. That said, it should not matter how you bolt up the flywheel - it will be balanced.
You should be able to gently tap the pilot bearing into place with a dead-blow hammer and a socket that is a tiny-bit smaller than the pilot bearing as Spitfire Rick suggests . If you are unfamiliar with this type of hammer, they usually have a wood handle and a rolled-leather head or is made of orange-colored plastic with loose sand encased in the head.
I hope that this helps!