Sitting in neutral, motor running, clutch out - there will almost always be a little more noise than clutch in. Reasons are:
- - Mainshaft and countershaft are in neutral position, no drive or driven gears are engaged for power output.
- - Clutch lever is out, so the clutch is transferring motor RPMs to the mainshaft, and turning it at speed.
- - Mainshaft is receiving engine power, countershaft is not turning at all - but it's free-wheeling gears are spinning becuase the mainshaft gears are turning under power
- - There's some slack in the slider gears and free-wheeling gears on the main and counter. Has to be for it to work properly.
- - You pull the clutch lever in, and you just cut motor power to the Mainshaft - the mainshaft will stop turning after it spins down.
- - Clutch lever in, the Mainshaft and countershaft gears aren't turning, so there's nothing in there to spin and make noise.
That may or may not be your issue - but that's why there will be a little more noise in neutral with motor running, clutch out, vice motor running, clutch in. When you're in gear, clutch out, you've engaged a drive and driven gear, and you're transferring power out the countershaft - they usually won't make noise then, due to being in a gear. It a constant mesh trans, so all drive gears are touching all driven gears all the time - everything is turning.
Could be a worn c-clip holding one of the gears on the main or counter, letting one of the gears move around a little more than it can/should. Could be nothing out of the ordinary, too. If it's anything crazier than that, post back about it. Broken gear teeth sound WAY different, both in and out of gear.