Clunking sound after revving engine

It may be time to get your valves adjusted. The reason you don't hear it after revving is that it may be coollig down enough to not make any size. What you don't want is the valve closing up on you, it could damage the came. Get the valves check, or do it yourself. That's where I'd start.

Oh yeah, straight pipes have to have the carbs jetted for that. You can burn the exhaust valves. Either bring it to a dealer, or get the Factory Manual. You can find them online for free in .pdf form. Not allowed to post links. Get a Kawasaki Factory Service Manual, not some Hayes, or Chilton. If you don't know how to adjust valves, best if you bring it to someone, or really commit to it. Get a proper muffler for that bike. I'm sure there are a ton of them on EBAY, and they made so many of those bikes, they can had cheaply. You'll get more power too, as you lose a lot of mid-range with straight pipes, especially if the carbs are set up for it, carbs of fuel injected, it has to be set up for that.

On deceleration, usually it is a hydro carbon backfire, which is unburnt fuel exploding in the tail pipe, indicative of a lean condition, and possibly burnt valves. A compression test could help you tell where the valves are. I sincerely doubt that it would be the chain, you should lube your chain after every ride, the sprockets last much longer.

First thing you should do is tune your bike up. Put some mufflers on it, in case it isn't too late.