Geo Tracker Transmission Whining

[fixkick]

Hello,

Got a soft top 1996 tracker, 2WD 5 speed manual 

The person I bought it from over a year ago had the transmission re-manufactured, and put in a new clutch at the same time. 
Since then, I noticed there was balking and hard to shift symptoms. I noticed that the clutch cable was tightened bit too much (not enough free play). Since then,
I replaced the clutch cable, put in some Penzoil Synchromesh, and just to be on the safe side I replaced the 2 plastic pieces at the bottom of the shifter. I adjusted the clutch cable free play perfectly, so that theres 1/2 inch play at pedal - and the clutch release arm itself has a tiny bit of free play as to not damage the TO bearing. 

Now, the car drives and shifts very smoothly. However, when I first start up the car in the morning, I hear a "whining" sounds coming from below the gearshift assembly (assuming its coming from the transmission). The whining sound is louder when I start it up in cold mornings, and the sound is only present when the clutch is not pressed in. The sound is present in neutral and when in all other gears, but once I press the clutch in the sound goes away. 
Additionally, after the car is fully warmed up, the whining sound is completely gone (not minimal sound, but the sound is completely gone). 

I'm assuming the sounds could be from a bad throwout bearing? Or can the sound be from the input shaft bearing? Which one is the likely culprit?  
I'm just a little confused as to why any of these bearings could possibly be going bad so soon after the transmission and clutch were fully rebuilt. 



Any advice would be appreciated; I've never done a clutch or transmission job, so I don't know how easy it would be to change out the bearing(s).

Thank You

"but once I press the clutch in the sound goes away". in neutral is key ,here. as only pilot shaft and cluster spins in neutral
what happens if you just press pedal and take up that slack only? at the pedal this gently presses the throw out bearing only (?) (just slack gone)?

seems like 1 of the 3 main bearings in the box are bad.
bearing 3/2,27,29,31.
but one other thing can make noise of any shop ever touched bolt 54, if this is not calibrated right the 2 gears bind. (35/50) reverse.
the book is not clear on these parts,54.  what I did is (never remove 54) I loosen it and try to get the gear 50 centralized,  by tapping the bolt 54, from sides.
even trying to do that in neutral, idling. so tap the head of 54 at say 4 points on the compass. 90deg apart and one hit may make it quite or will self center and go quote.
removing 54 bolt trans box in car , invites dropping part 52 into to bottom of case,  no fun that.

in neutral shaft 7 is stalled. (car not moving.) so neutral is the best test.(if fails and does)





this part below is very tricky to setup. box split i just adjusted the bolt until the 2 gear turned clean and free, no binding up as it loves to do.