That's a completely different story. The rpm difference when shifting from first to second in the transmission shafts is always substantial and since the transmission doesn't have scyncronizing gears, there will always be a substantial "CLunk". You could try just slowing down your shift with your foot and allow the secondary shaft a chance to slow down, and what I mean by that is run it up in first, back off the throttle as you pull in the clutch and hesitate the shift into second. Think of it as shifting a car without using the clutch. As you pull it from one gear to the next, pause in neutral and allow the transmission a chance to slow down so the next gear scyncronizes before pulling it into the next gear.
If there's a slight drag in the clutch pack, it will also cause more of a clunk or in your case, ticking and then the clunk so you may want to just check the clutch adjustment and the critical check is the lever point on the actuator. If you look at the lever, it should be past 90 degrees to the cable so that when you pull in the clutch half way, the lever is 90 degrees to the cable. That way you achieve the most rotation of the clutch actuator for the given pull on the cable.
The only other check would be to inspect the clutch basket for notching. If the clutch plates and fiber plates get stuck in a groove, the plates will not completely disengage and again, you'll experience some difficultly during shifting.
hope this helps,
KB.