I have a 2011 Ultra Classic with the Profile Low Touring Shocks on it. Last weekend I installed a rear end lowering kit. The kind that lets you move the rear shock mount back up to 3 inches., the shocks are at the 2" setting. With 40#of air in the shocks, my wife & I made the return 60 mile trip home with no problems. This week, driving back & forth to work, on every bump there is a clunk in the rear over every bump. It feels like there is no air in the tire, or no shocks on the bike. I checked the shock air pressure, tire pressure and all fittings and everything seems ok.

Any ideas?

 

So you have lowered your bike 3"...........1" with the shocks and 2" with the lowering blocks.
That sounds to low to me.

On another note I had a clunking sound and the rubber bushing that is in the rear muffler mount had sliped out.
So the muffler could move up and down a 1/2".
This is a common thing with Monster Ovals, which is what I had at the time.

 

You could try backing off one notch on the lowering kit and take a ride, to see if the problem goes away. If not, remove it completely and try again. The main thing at this stage is to identify where the problem is coming from.