I use lingodeer together with duolingo. Libgodeer is really good for pronounciation. When doing the reveiws (or training) you can choose between listening, word or sentence exercise, which i believe is awesome, since i can choose what i need to get better at :) The buggest downside of lingodeer is the community ^^

Seems like they added this feature recently (12-09-17)

Untill they add that, I suggest using the power of the internet! Searching these things out usually isn't to hard to find. The easiest, though maybe not the most accurate thing I use for quick finds is google translate since it writes it in Romanji at the bottom. Wish it was written Hiragana instead of Romanji, but whatevs, you still get the pronounciation.

I wish I could click the letters for individual pronunciation

Taking notes of all the kanjis and their pronunciation helps a lot. Don't just make the exercises, threat them like an actual class

At one point Japanese adopted a lot of aspects of the Chinese language (including the kanji of course), so you get this situation where a character can have multiple readings - kun (Japanese) and on (Chinese) pronunciations. Which one you use depends on the context

So you've learned the basic numbers, いち、に、さん etc. - these are actually on readings, "Chinese numbers" if you like. They're the readings you usually use, so don't worry about it too much. But Japanese has its own original numbers: ひとつ、ふたつ、みつ　and so on. They're not used much now, but they do pop up in a few places - and counting objects is where you'll tend to see them

The main one is the generic counter - one thing is ひとつ, two things is ふたつ. In Japanese when you want to count things, you have a number and then some "counter" word that describes the object - "person", "long thing" and so on. The generic counter is for when you want to give a count without getting into what it is

Another place you'll see them is with the counter for people - 一人 is ひとり, 二人 is ふたり, 三人 is... さんにん! Yes it's back to the Chinese on readings, with a different reading for the counter too (‐り is kun, にん is on) - this probably reflects that Japanese stuck with the old way of referring to one or two people because it's more tightly woven into the language (ひとりで means alone for example), but adopted the Chinese version for counting in general.

It's more complicated than that (languages usually are) and I'm definitely sketchy on the history, I just wanted to give you a general feel for why you sometimes get different readings for things. Gennnnnerally single-characters will use the kun reading, and multiple kanji represent a word from Chinese and use the on reading. So you can expect each character to have at least two pronunciations, but it depends on the context!

Certain counters modify the way the kanji is pronounced

Not sure why the readings differ in those two cases specifically, but each kanji has multiple readings. 一 can be pronounced いち or ひと depending on if it is with hiragana, other kanji, or other factors.

There are multiple forms to count things.

This is a case where Japanese breaks the rules. In a similar situation, 一人 is pronounced ひとり instead of いちじん。My take on it is that is using the kun reading of 一。

Both ways should work. I have answered both ”椅子が一つあります” and ”一つ椅子があります” and gotten it right each time.