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New whine after having trans apart, normal?

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I've had 2 other transmissions apart before this one, a 2wd Impreza trans and a 2wd GL trans, same as this one basically. I had it apart to replace the input shaft seal and after filling it up with fluid, getting the motor in and everything ready to go I fired it up and took it for a ride I noticed it was shifting hard and noticed with my hand on the shifter I could feel a high vibration that wasn't there before. I didn't have this experience with the other 2 transmissions I've had apart, they were pretty smooth afterwards. Do I have anything to worry about? Will the whine eventually go away and the shifting smooth out? I adjusted my clutch cable until it grabs towards the top of the clutch movement so I know for sure it's completely disengaging the clutch. For what it's worth, this is the original thread: http://www.ultimatesubaru.org/forum/topic/140724-input-shaft-seal-84-dl-what-else-while-its-apart/

 

Thanks for any input.

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Thought this might be important... the passenger side axle pin wouldn't go in so I really pounded on it and only got it halfway through. The hammer was literally just bouncing off the pin. Could that damage the roller bearings in the front diff??

 

BUMP

tap the pin out and rotate the shaft 180 degrees to see if it lines up better. I just got done with 2 new front axles , there is a slight difference in thread count between each hemisphere that the pin holes divide.  I would double check that. might as well put new pins in while your down there if the originals are mushroomed in the slightest from hammering them. I dont know if it would damage bearings but I would think you would need to be near thor strength to break or bend the bearings

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