In my experience that its cost and effect, most if not all nitro RC's have a clutch and a brake, clutch severs the connection between the transmission and the motor and the brake stops the rig from moving forward. When electric rigs brake ESC locks the motor which means everything stops spinning your transmission connected to the driveshaft connected to the gears in your differential and to the wheels. And if you double push the trigger upwards it gets worst coz now the motor reverses on the second upward push and puts more strain on high speed rig moving forward to an abrupt stop to reversing. Now heavy breaking at high speeds and take into consideration the weight of your rig it takes a heavy toll on your gears not to mention your driveshaft, gears in your transmission, spur and pinion gears. Take the transmission spur gear cover off and you will see some metal dust or flakes in there, even when you mesh it right you will still find dust and flakes a by product of heavy breaking from high speeds. Inside the transmission the grease on the gears turns dark because of the metal dust and it has nothing to do with meshing it right, it gets darker faster with heavy breaking on high speed.
Now some might say that other electric RC's in the same class or bigger doesn't have this problem, well lets take the Losi DBXL with the electric conversion and this is just an example, no clutch no break but hardly have the clicking problem on high speed heavy breaking. DBXL is heavier, bigger and wider the difference is the spiral cut bevel gear which the YXL does not have, but even so you do heavy breaking on high speed often enough it doesn't matter how your gears are cut sooner or later it will be clinking.
This is just based on my personal experience and like you I looked into other avenues that could have contributed or may have been the cause of the clicking, pursue them too I have broken front and rear bevel and pinion gears from doing the exact same thing you did it took me 3 sets to figure out that it was my driving style. Luckily Axial support was/is there to replace broken parts, you should call them for warranty replacement and finally if your not working on your rig your not really having fun.
