I would say 99% input shaft bearing as Sobo stated.
Remember that one time your shifter linkaged was held on to your trans with vice-grips? lol.
Wasn’t me. You must be thinking of Josh. 
HAHA was, whos to say it still isnt! and it was the clutch line because the pressure plate from the twin disc was shattering the plastic nuts.
It’s been a couple years since I last saw it, but if I recall correctly it was in my rear view Buy Drew’s exhaust fggt!
Andy, is this thing going to be done anytime soon or what?
Can I have my pliers back? 
input shaft bearing shouldnt have any play.
im down to take a look at it if you’d like. had a hand in rebuilding one of these a couple years ago in school, pretty sure i still have my manual trans text book around somewhere too if youd like to borrow that to thumb through.
Appreciate the offer. Case already reassembled. You can check out the old bearing if you like. Thanks though.
Pretty much got everything back together. Just need to tap a couple pins into the shifta box, pop a cover on inside the bell housing, and smash it into the hole under my car. Was waiting for some sensors, new u joints, driveshaft balance weight welding (loosened up somehow), and exhaust downpipe gaskets. Hope to have it at least driveable by Sunday.
:tup: if youre looking for a hand getting it back in let me know. im always down to wrench.
Me and Rob are gonna try this weekend. Not sure which day. You can stop out and be beer supervisor if you like. 
did you find an obvious problem with it?
Since the throwout bearing was virtually new and seemed fine, I’m gonna go with input shaft bearing. Just nned to bleed the clutch and test.
It might be a little late but the whine is usually caused by excessive gear lash(space between the gears as they rotate). you can check gear depth in the trans using layout dye and adjust using shims to adjust the gear sets on the input and output shaft. EDITED OUT WRONG INFO
here is a diagram on reading layout dye on a gear, its for a ring gear but the same basic rules apply. 
you will need to apply a load to the gearset so that it requires about 40-50 pounds of torque to spin the gears
here is what it will look like when backlash is set correctly
Drive pattern
Coast pattern
And here is what it looks like when its incorrect - Drive-side contact pattern - top / heel. The dark area on the yellow is where the pinion and ring-gear have come into contact, removing the marking compound from the teeth and illustrating the contact pattern. In this case, it is on the drive-side of the ring-gear teeth and is clearly towards the top and at the heel of the teeth, illustrating that the pinion depth is way too shallow
Coast-side contact pattern - top / toe. Dark area illustrates contact pattern on coast-side is at the top and towards the toe of the teeth. Pinion depth must be significantly increased and backlash set to spec
Manual transmissions are a little easier since, as long as the bearings dont have any up down play, all you need to do is set the gear depth or basically the fore and aft position of the gear sets in the case. the only problem is that there are 6 gears to check in the case as opposed to one in the rear.
Hope it helps let me know if you have any more questions
Edite: this should help also
REALLY wish you would’ve posted this about three weeks ago. Pics not showing up in your post. What might cause this type of situation to arise? What are the possible consequences if left alone? Would really like to feel good about this tranny again. Thanks for the post.
haha I would have but i wasnt here 3 weeks ago :D. wear causes it, hard launches, hard shifts, horsepower, etc. Worst case scenario if left alone, you’ll have some missing teeth on the gears on both the input and output shaft. best case scenario, your annoying whine comes back if anything happens at all. the more power, and more abuse that the car sees the more likely it is that you will move closer to the worst case scenario.
I lied to you about the crush sleeve I had rear ends on the brain.
either way with or without the crush sleeve if the trans isn’t shimmed properly you can have excessive endplay in the input shaft which will basically cause the same thing to happen. GM recommended endplay tolerance range is only .000 to .004 and without shims they have about .030-.060. And honestly .004 is too much because the aluminum case expands when it gets hot. Try to keep them between .000 and .002.
IF the whine was in the bearing you may not have a problem as long as everything was put back together correctly. If the whine was due to wear in the transmission its self the bearing going bad could just be an indicator that something else was starting to go wrong or the bearing just decided to take a dump. If the whine was in the gears then the damage is most likely already done, and it will give you problems down the road. Since the transmissions are fairly easy to do on these I would pull the trans out and check the input shaft endplay. If its within tolerance and the whine is gone. you’re most likely good to go. I would only recommend layout dye on the gears if you were going to split the case again.
Ha I found it buried deep within my bookmarked pages. The tremec t56 service manual-http://www.ttcautomotive.com/English/onlineorder/pdf/LD56-0610-0199_2.pdf
here is the page with the pictures that didnt show up
http://www.pirate4x4.com/tech/billavista/Gear_Setup/
Curious as I have rebuilt a number of T56 transmissions and never have seen a crush sleeve?
HA
see previous post. Ive been awake for a day or two :P. and its been monday here for 6 hours
My take on it is this. When it was apart all the gears and internals looked normal upon visual inspection but without a gauge, I would say shaft end play is more than evident. I’m not sure I wanna pull this thing out again. I just got it back in a couple weeks ago. This sucks.