I posted this a while back on a similar post and I suspect what you are experiencing is an alignment problem. I have used a procedure for mounting a rear tire on any Venture that will align the rear end perfectly every time. I was told about this proceedure by a Venture mechanic back in 89 or so and have used it ever since.

1. Before removing the tire, put the bike in gear.

2. When removing the rear tire, loosen slightly the 4 - 14mm nuts to the rear member. This will also give you a little wiggle room to remove one of the wider tires.

2. With the tire off remove the 4 - 14mm nuts and remove the rear member and drive shaft. Grease the drive shaft splines and slip it back in the drive tube. This can be a bit tricky but feel for the inner spline U joint and move it up and rotate it where the drive shaft enters the U joint and the studs enter the holes. Put the 4-14mm nuts back on but leave them a bit loose.

3. mount the wheel into the rear member. Grease the axle lightly and slip it into the wheel through (1.) the large washer and (2.) the caliper bracket. Tighten the axle nut to where it pulls the axle through and snugs into place and then loosen the nut. With a 10mm allen wrench, you can rotate the axle. Turn the axle until you feel a loosest spot around the circumference of the axle. Mark this spot at the pinch bolt slit with a file for future alignments.

4. With the axle pulled through and snug, tighten the pinch bolt and then torque the axle nut to 110 lbs. This gets the axle and inner wheel splins into perfect alignment with each other.

5. Now go back with a good 14mm boxed in wrench and tighten the 4-14mm acorn nuts on the rear member in a cross pattern. This now pulls the drive shaft into alignment with the rear member.

6.You are finished with this part and can now put the caliper back on along with everything else that you took off.

Now you really don't need to go through this entire process, but you do need to raise the bike where the rear wheel is off the ground and loosen everything up as follows:

1. Raise the bike with the rear wheel off the ground.
2. Loosen the axle nut completely.
3. Loosen the axle pinch bolt.
4. rotate the axle until you feel the loosest spot and mark this spot on the axle at the pinch bolt slot.
5. Loosen all 4 - 14mm acorn nuts from the final drive assembly.

Now you are ready to tighten it back up starting with:

1. The axle to the point the axle nut just starts to tighten.
2. Tighten the pinch bolt
3. Torque the axle nut to 110 lbs
4. Tighten up the 4 - 14mm acorn nuts in a cross pattern.

If it's still making a clicking noise then take it back to the dealer and have them look at it. If the rear fluid was not flushed at 500-1,000 miles, then you might have a set of needle bearings going bad in the final drive