PureBlood

1993 Del Sol Si
Its difficult to describe but I'll do my best
When in neutral, my transmission makes a whirring, clicking noice, however if the car is in any gear and the clutch is to the floor the noise is not there.

Also, when accelerating / decelerating in any gear, transmission make a whirring noise (different noise than above)

I know this isn't much to work with, but any ideas would be great.
I've already checked the tranny fluid / had it flushed, bled my clutch, Reset my ECU.

Car has 106,000 miles on it and the noise has been there since i bought it. Is this typical or ?

6.5inCivic

Sounds like your bearings are in very bad shape. There are 2 bearings on output shaft and 2 bearings on counter shaft. Could be any or all of them. If the tranny makes noise while driving then they are really bad. I had my changed because it was making pretty much the same noise. At first it was only in neutral then noise increased during driving.
I hope that help answering your question. As to fixing it! Need to take your tranny out and have it rebuild. If you already have it apart you might as well change stuff that look pretty worn out.
Good luck