I sent a message to you about this as well, but just in case somebody else is having this problem, I would like to share my experience with this problem.  The vacuum slide on the carb is the problem if it is a stock carb.  When you go over a whoop the slide moves causing your bike to cut out.  I fixed the problem by installing a FCR carb. 

Also, another person said their bike was still running after the key was turned off.  It is a common problem due to the fan running when you shut the bike off. 

Another problem you may encounter with a z400 is the reverse rev limit switch down by the shifter will make one cut out as well.  I cut my wires and bypassed the switch to fix that problem.

I have had a z400 since 2003 and have encountered most problems associated with it.  Hope this info is useful and if you have any more problems feel free to send me a message!
Steve