Rear brake "knocks" & brake pad wear

Hey guys, hope you can help. I have a '82 XJ650. I recently got new tires front and back. In putting them on I encountered a few issues that I could use help with.
1. The back break now "knocks" when I press it when moving. When sitting still it seems to operate as normal. When I am moving and try to stop it knocks. It seems to work OK but I am not sure why it knocks once when the brake is applied. I'm sure I put it back together wrong but I have tried again and again and keep getting this.
2. The front break pads are wearing very uneven. The pads almost have a wedge shape to them. What would be causing this?
Thanks for any advice!

 

Not sure what's up with the rear brake, but the front pads being wedge shaped is normal - they came out of the box that way.

 

This link may help to ensure you've got the rear brake assembled correctly.

 

Well maybe it is time to tear it down again. But now I have a new problem.
In my ride today my front break pads just plain fell off. I could not recover them and will need to buy new ones.
I am pretty good at working on cars but when it comes to bikes I must suck.

 

Well, something's definitely wrong if they fell off and away from the bike. The pads should have a hole at the bottom of the pad where a through pin goes through. If that pin is installed, there's really no way the pads could have fallen off. Here's a picture of the assembly.

I've got a new set of EMGO (#91-62205) pads in front of me. I see they come with a new pin and retaining spring. Hopefully you didn't loose the antir-rattle clips.

P.S. Here's a link to the Yamaha site where I'm getting these pictures. Bookmark it. It's very helpful.

 

Well that would explain it. I still have the pin but it looks like it worked out enough for the inside pad to fall off. Not sure if there was a retaining spring before or not but it is gone now.
Where did you get your pads with the new pin and clip?

 

Ding ding ding ding, introducing one more of your XJ's best friends, Chacal! Most likely has your part in stock and ships promptly.

 

OK, well that more or less sorts out the front break. Anyone have an idea on the knock on the back break? Looks like I put it back together like the diagram shows.

 

Perhaps the noise isn't the rear brake, but something in your final drive. Have you tried putting the bike on the center stand, starting it, putting it in gear so the rear tire spins, then engaging the rear brake to see if you can see where the noise is coming from? (Be carefull!) I'm wondering is something has come loose and the weight tranfer from acceleration to deceleration is what you're hearing.