You won't be able to change the pilot bearing by just sliding the transmission back on guide pins (unless they're REALLY LONG!
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You'll need to use a slide hammer to pull the old pilot bearing out of the crankshaft, and the transmission will be in the way of that. You can remove the transmission by disconnecting the u-joint, and pivoting the torque tube up out of the way, and then pull the transmission back and out. It'll have to come back at least 8 inches or so (the length of the input shaft in front of the transmission case.) Then the clutch pressure plate will have to be removed. That will give you enough room to either use a slide hammer or the hydraulic method to remove the pilot bearing. The latter consists of stuffing the cavity of the pilot bearing full of bread, or grease, and driving a close fitting shaft into the pilot bearing. The hydraulic pressure will push the bushing out.
