Ouch!  If the whine is in direct proportion to road speed it's the pinion .

 Whatever it is, it's time for a rebuild while you still have a rebuildable unit.  Driving too long on a bad pinion bearing will destroy the ring and pinion--$$$$.

Some aftermarket bearings have had problems, so go with GT or AA Transaxle for the rebuild.  

Good luck,

Stuart

-----Original Message-----
From: Vanagon Mailing List [mailto:vanagon@gerry.vanagon.com] On Behalf Of Geneva Saint-Amour
Sent: Monday, July 28, 2014 5:56 PM
To: vanagon@GERRY.VANAGON.COM
Subject: Clicking noise/whining noise

Hello all-With your feedback and support we did some repair work on the transmission and drivers side axle.  We replaced the entire right axle and CV joint with an new axle.  That was repacked when replaced.  We also drained the transmission and replaced fluid with Sta-Lube GL4 gear oil.  
Now we have a whining noise from the transmission when under load.  AND a clicking sound when NOT under load.  
Ideas, suggestions, help?
1985 Vanagon with manual transmission, Bostig engine

☮ ☮ ☮ PEACE ☮ ☮ ☮Geneva Saint-Amourwww.slowcarfasthouse.com