as you can image,there are always dozens of regional dialects and such, and even speaking Japanese is hard.
one of the most difficult challenges of speaking Japanese is the different tones. We learn the tone of each character as we acquire vocabulary, but it is difficult to remember these when speaking.it is really not an easy thing to speak Japanese correctly.
But it is okay,although it is not easy to do,but we can learn the way by our brain.it is important to internalize the tones as part of phrases.actually,listening helps you do this.
by the way,the intonation and rhythm of Japanese, or any other language, can only come from listening to the native speaker. You can not learn it theoretically.but you can still learn it systemly.