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That also just happens to coincide with loading and unloading the throwout bearing. How long does this "spin up" take? The input shaft will go from stop to engine RPM in a fraction of the clutch travel. It should be nearly instantaneous. If it takes longer than that, it is not the input shaft you are hearing. That does not necessarily rule out an internal transmission issue, but it rules out the input shaft bearing.
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It IS near instantaneous, and yes it occurs during that tiny fraction of pedal travel where the clutch re-engages. The sound also corresponds with the mechanical thunk you can ever so slightly feel when the input shaft is spun up. I promise you it is related to the input shaft spinning up. It might be something else connected to the input shaft, as you mentioned below, but it's definitely related to the input shaft spinning.
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Now, you said that the noise goes away clutch-in. You presumably have the clutch in when you are shifting...? So describe this a little better... Does the noise suddenly come back? but only during the shift? Because that points to another problem entirely.
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You are right in that I do have the clutch pushed in when I shift. However, this is different than what I mentioned earlier with the transmission being in neutral because the car wasn't moving so pressing the clutch allowed the input shaft to stop spinning.
When I'm changing gears, the input shaft is spinning at high speed with the shifter in 1st gear. I then depress the clutch pedal and shift into 2nd. During that period, the clutch is depressed, but I hear the sound because the input shaft is still spinning. And what I hear is the decrease in speed as it decelerates rapidly as I engage 2nd.
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Not necessarily. Adding a thrust load to a worn or failing bearing can silence it, for largely the same reason that pushing on a loose, rattling panel can stop the noise it's making. In fact, most people reporting TOB issues say the noise starts clutch-out after cold start, and only progresses to happening clutch-in when it gets really bad.
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That's an excellent point. I suppose it would make sense for the unloaded bearing to make more noise, since there is no load to silence any free play and dampen vibrations.
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It doesn't have to coincide with the actual gears; consider this... All the gears in the transmission are in constant mesh. They are all spinning at the same time, and they are all in mesh regardless of the selected gear. 2 pairs of gears carry the load at any given time: the selected pair on the layshaft and output shaft is the first pair, the second is the the input shaft gear (there is only 1 gear on the input shaft), with it's corresponding gear on the layshaft. The latter pair carry the input load regardless of the selected gear. With the exception being in fifth gear, as that connects input and output directly. 1:1 Oh, I forgot to ask, does the noise go away in any gear?
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The noise doesn't go away in any gear, to my knowledge. I'll have to pay more attention though, but I know it makes noise in at least 1-4.
Also, what you stated is exactly why I figured it must be input shaft related. Since all the gears in the transmission are always turning together, there is nothing in the transmission that rapidly decelerates when I shift from 1st to 2nd, or 2nd to 3rd, OTHER than the input shaft and its gear, since they have to match engine speed. So the fact that this whine does that seems to rule out everything except the input shaft, as far as I can figure.