[Ken Bergen]

Thank you for the fast reply.

I just want to be clear as to what you are describing. I have take a couple pictures of the original (now off the bike) final drive.

When you say "the drive shaft most likely came out with it". Do you mean the gear that matches up with the part I am pointing to in the first picture?

The part that you are describing as the "universal" on the engine side of the "accordion boot". Is this what is in picture 2?

The part you're pointing to is the drive shaft that glhonda referred to.

The universal joint is inside the boot between the engine and the swingarm.
It can be difficult to get the drive shaft splines you're pointing to mated with the u-joint and sometimes the u-joint will pull off the engine output spline.

You will have to pull the final drive and with the boot pulled back re-install it making sure the u-joint mates both with the drive shaft and the engine output shaft.

 

[Ken Bergen]

As glhonda said you've done nothing that is going to cost you more money.
Just wait for his etch-a-sketch drawings:ROFL: and all should be clear.

 

[Ken Bergen]

Checking your first post your expert may have been wrong.
If the output splines on your old drive are badly worn that may have been the source of the clunking.

If the splines on the donor drive and or the splines on the drive to wheel coupling you used are are worn it's likely it will still clunk.