I get a clunk over bumps from my speaker box as well, but it only happens if the box gets air and then it comes down with a..... clunk =Happens over speed bumps but not during every day driving.
You may also want to check on your shocks to make sure they are in good order.
2001 Ironman Daily Driver... 3.5" suspension lift (OME912 springs and 1" spring spacer), ball joint flip, 1.5" front diff. drop, 33"x12.5 TrXus MT, 16x10 Eagle Alloy rims, Interceptor, PV muffler, K&N air filter, Alpine Supercharger, Bilstein shocks, and some trimming.
2000 Ironman Project LS-1 VX... very slow progress but someday....... ohhhhh someday......