I just bolted up a 700R4 to a ZZ4 350, and the flex plate bolts up to the flywheel, then with the torque converter properly indexed to the front pump, the tranny blots to the block, and the torque converter to the flex plate. The pilot bearing doesn't come into play at all, and can remain or be removed, your choice.

For removing, you can pack the void with grease, and using a bolt ground down to near the OD of the tranny shaft end, use it as a hydraulic ram to push the bearing out without damage. Here's a link - https://www.google.com/search?q=remo...O7tQbL1r2gBQ21