On my 1000, the pilot pushing assembly is driven into the drive cup. Then you put the flex driver disk on.
Here's a picture. The center hole in the drive plate should be larger than the flange on the pilot bushing, so you can remove the drive plate leaving the pilot bushing assembly in place. If your center hole in the drive plate is smaller, then you had to do what you did--you wouldn't be able to do it any other way. If it's in there and working, then I'd leave it alone. It will be many years before you should need to remove it.
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