Twice now I have been driving along and all of the sudden bam I get a REALLY loud whining noise like Im going 30mph in reverse. It makes the noise wheather im in gear of nuetral clutch in or out then after a minute the noise goes away. What could that be?

 

Take your supercharger off of it.

But in all serious it could likely be something going to **** with the gears.
Might want to take a look at your oilpan and see if there are any metal or other debris in there
Is it whining or whistling?
Also any other symptoms with this? Shaking? Bogg downs? Slowness?

 

No other symptoms. I just swapped this tranmission in because the old one had a worn input shaft bearing. Could one of my axles popping out make a noise like that? It seems to me if its making noise in neutral then it shouldnt be the transmission.

 

If it's neutral than it shouldn't do it with the axle unless you're moving. Does it do this while standing still?

 

The input shaft is still spinnig in neutral, ^^^^^^this question needs answering first though.

 

No not while standing still

 

Could be the axle. Was the clip still on the axle when you put it in?

 

No i dont remember any clip. Does the clip come out with the axle or does it stay in the transmission?

 

Think talking about C clip
http://www.justanswer.com/honda/24gm...all-joint.html