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"Clunk" When 2-1 Downshifting

It was my understanding that the upper gears were synchromesh but first was not.

They are all the same -- 1st is not different.

My 06 Gold Wing had a very loud clunk when downshifting. I asked the Honda dealer about it and he said they all do it and it is because the gears are "straight cut". Maybe this is the same on the RT?
That's nonsense (your dealer's comment, not your post). The gears are constant mesh, straight cut except 5th, which is helical (15 or 17 degree angle IIRC, depending on year). Straight-cut or helical constant mesh gears don't change the dynamics in the tranny. The significant change in output shaft speed and input shaft speed associated with the 2-1 shift results in heavy parts accelerating/decelerating greatly, and the gear engagement dogs taking some big hits from their mating recesses as they try to engage the 1st gear gears with relatively high speed differences -- and a clunk is born. That's why waiting to downshift until you're at low speed helps -- leas speed difference between the shafts and the gears to be locked to the shafts.
 
It was my understanding that the upper gears were synchromesh but first was not.
Actually - calling them "synchromesh" isn't totally accurate - all are "constant mesh" - meaning the gear pairs are always engaged with their mate.

Power transfer is done by sliding the gear a small amount so "dogs" on the sides of the gears can mate with matching dogs on the side of other gears, or by sliding a locking disk (locks the gear to the shaft) to it connects with the dogs.

Bike transmissions are generally a quite different beast then automotive transmissions (which use synchronizer rings to bring gears to matching speeds so they don't crunch when mating. No synchronizing rings on the moto transmissions.)

See: http://www.gadgetjq.com/transmission.htm for a simplified explaination

It is correct that there is no difference between 1-2 and upper gears except neutral is between 1-2..
 
Auto and MC transmissions are pretty close in that both are constant mesh (other then reverse which can be gear to gear using an idler gear) The auto does add synchronizers which are basically brakes. An MC trans would be too bulky if they added them. I believe BMW is using helical cut gears in the RT, quieter but not as strong as straight cut. Has to do with line or point contact, stuff I just don't remember. Anyway the noise is caused by what was mentioned above.
 
Clunking 2 to 1

My last two Hondas did it and they were noted for great transmissions. Actually, going from N to 1 while cold is so much better on the RT than the ST1100 and ST1300 but that's another issue.
I've always done what is stated above... wait until I am going below 10 mph before shifting to 1 and only if I need 1 otherwise I wait until the bike is hardly rolling to downshift. I'm also learning to use 2 more often on slow turns when the bike is always rolling (not from a stop).
Btw, I do a lot more shifting on the RT than I ever did on the ST. That's the first thing I noticed when I rode the RT for the first time. Must say that V-4 is an awesome engine.

tsp
2010 R1200RT
 
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