Ive been shopping around for 2nd g fits with manual transmissions. the problem is, every single one i test drove with all differen miles all made the noise from the transmision it got me wondering is this just normal noise? or is the input shaft

 

My Fit is an automatic, so I haven't experienced the noise you're referring to. My last car was a 2003 Civic SI with a 5 speed manual though and I didn't have the noise with it that you're referring to here. Is the noise you're referring to from the input shaft bearing or could it be from the throwout bearing? The throwout bearing can make that type of noise also if it's out of adjustment and is actually riding on the pressure plate instead of maintaining clearance except when you push the clutch pedal in and it engages with the pressure plate.

I'd suggest going into your local Honda dealer and talking to the service dept about the issue. See if it's a normal sound with the Fits or if they've serviced any stick shift Fits with that noise. Perhaps they may even have a Gen 2 stick shift Fit on their lot they can start for you and check. Good luck!

 

no its not the throwout bearing. a bad throwout bearing would make noise when the clutch pedal is pushed in, and stop when it is released.

 

Not sure about that -- What you described sounds like a failing throwout bearing.
When my TOB was going bad in my FR-S, it was squeaking when the clutch pedal was up, and the noise would go away when the pedal was depressed.

That being said, my 09 GE w/ 170k miles doesn't exhibit a noticeable TOB sound and I believe it is still on the OG clutch. I never ride the clutch and it was previously a 1-owner car when I bought it.
I get more of a creaky noise from the CMC, which I lube from time to time.

 

I'm also unsure in regards to the noise source here. I replaced my clutch at approx 80k miles and didn't touch the output shaft bearing. There was nothing in the manual's procedure for clutch replacement that mentioned it, and I knew my problem was in the clutch (take-off shudders.)

The noise you're referring to isn't a standard thing. the first car you drove had a good number of miles on it and may need the clutch serviced. The two that followed didn't have enough miles on them so to speak, and probably sat a lot. Grease gums up on sitting vehicles and, in my experience, they can be even more of a pain v. higher mileage ones because a bunch of random stuff will start exhibiting faults when operation suddenly increases. I've replaced far more bearings on sitting vehicles than ones that were driven regularly.