Three hours should be more than enough, but not only do you have to clear immigration and customs at HND, you need to change terminals from the international terminal to the domestic terminal (either 1 or 2 depending on which airline you are flying), but that is still enough time to accomplish it all, just a bit of extra work.

If you consider the time (3 hours plus effort and flight time from HND to ITM), flying into KIX directly would of made a bit of more sense, since you can clear immigration and customs right at KIX and then proceed by train or bus to your final destination in Osaka or Kyoto so it's less work than the change required at HND.