No pilot bearing!!! That can't be good.
I believe the main reason is to support that end of the input shaft but also to align the shaft to the crank. I hope you have not damaged anything by running without it. The vibration you mentioned was probably putting your tranny through more abuse than it should normaly see.
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Al, 94 Mustang GT
3.55 gears
Magnapack mufflers with 2.5" tails
STEEDA TRI-AX Shifter
MAC pulleys
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