Whine is more often related to gear mesh than to bearings....BUT, a bad bearing can throw gear mesh out of whack.  In your case, the whine in all gears except top might point to a countershaft bearing problem.  Since when in top gear, power is being transfered straight down the main shaft of the transmission with no loads taken by gears on the countershaft.

The trans in my 280 had a whine in 3rd.  After a little poking around I found it was because ONE of the two gears that mate to produce 3rd had been replaced without it's mate being done so the wear pattern on the old gear didn't mate particularly well with it's brand new counterpart.

I'd have to look at the section views of the trans again to see if there's a single countershaft gear that's in mesh for all 3 reductions, and not top.  If that's the case, that gear could be your culprit, but I thought the R/1 combo used a whole different path than 2/3.....Hmmm....

It's also possible that the trouble is at the rear output and that the torque multiplication in the lower gears can stress that bearing into whining where the straight through torque form the motor alone isn't a problem.  Is your whining any worse under hard acceleration?  At level cruising speed/load?  Under de-celeration?

-Dave G.