How bad is this noise
 

See if you can diagnose this. Kind of a rattle in neutral. Clutch in noise goes away. In neutral move the shifter almost into 1st, noise goes away. Sounds bearing-like (Not really a shift rod banging noise, but that would be my choice if I get to pick the source). Noise also goes away if I give it some gas. When the noise is alarmingly loud, pumping the clutch a time or two can reduce/eliminate it.

Last winter I did my clutch could it be a bearing in there? Possibly tranny related (the noise really travels up and down the torque tube)? How about this, this summer I replaced my clutch master cylinder. I now have a good bit more free travel in the pedal, could this being out of adjust cause a problem that would make a symptom like this?

Any help or direction would be appreciated, thanks.

I have the same thing, but it has always been my understanding that --AND CORRECT ME IF IM WRONG-- its fifth gear rattling around because there's some weird design flaw with the transmission on these cars and it is normal.

if not, torque tube bearings maybe?

Throwout bearing?

I agree with yellowline, throw out bearing; although the throw out bearing is normally changed out at clutch replacement time. I think a bad throw out bearing may effect (damage) the pressure plate but not positive.

I honestly suspect the throwout bearing (which I did change with the clutch), but any other suggestions would be appreciated.

I kind of figured it was that noisy 5th gear thing, but it's gotten louder which makes me think that this should get some attention. The torque tube possibility is a consideration. I have a spare one I may try to rebuild and install if I need to pull everything apart again.

One more, if indeed it is the throwout bearing, since I replaced it with the clutch, what could cause it to go bad? Should I pay particular attention to something specific when I endeavor to replace it again?