engine vibration

I recently switched my automatic to a standard on my 1991 suburban 6.2. Engine starts & runs OK but when I shut it off just before engine comes to a stop it vibrates for a second or so.The flywheel & clutch & pressure plate came from a 6.2 that was in a 1985 gmc & there was no problem when it was in that vehicle. I used a brass bushing style pilot bearing instead of the type that has the small bearings which is recommended for the 6.2. Anyone have any idea what is causing this problem? It is my understanding that any vibration is very hard on the crankshaft so I figure I had better solve this problem before I start driving this vehicle. Thanks in advance for your help.