This story was in a documentary I saw a few years ago. In it they told about how the US dealt with this threat.

The balloons had an altimeter hooked up to a release valve for the hydrogen in case it went too high. They could also drop sandbags if the balloon was too low, thereby keeping it in the jet stream

So they had the following to go on:

So what were they to do? Well, this is where it gets strange.... After exhaustive searches of all the information they had about Japanese manufacturing, trying to locate where the components were being made the US specialists turned up.... Nothing.

Now we go back in time a little way, to a time when one of the emperors was dead keen on scientific research. Specifically geology. He ordered a gigantic geological survey of all of Japan. They catalogued the geological composition of every part of the country.

Right down to the sand on the beaches.

Come back to the '40's and the war effort: Someone somewhere remembered the geological survey which was squirreled away in some university or other such repository of knowledge in the United States. After some meticulous checking they figured out which beach to check. They found a factory there and bombed it.

As much as I think bombing civillians at random is really nasty, I think you have to admire the plan that the Japanese were trying, Not to mention the thorough approach the people in the US took to dealing with it. If no-one had died on either side it would probably be the best war story of them all.