I have great news for those who have already finished RTK. Remembering compounds is piece of cake.
Some will give you trouble but most of them stick after the first few reviews, for life. Much, much easier than RTK.
But as it is so easy, I did not developed a method. I go through them randomly, as I encounter them. If I fail remembering them twice, I make a place mnemonic (like in the movie method) and go on. Simple as that.
I have no data to show how fast I remember them, but I remember that there were times that I added comfortably 100+ sentences/day. I never could do it with RTK, so do your math.
But I still have something to point out.
First, you need to find room for the readings in your brain, just like the primitives in RTK.
When you first encounter a new reading, it will bog you down. It'll take some time to get used and after some time, it will be part of you and it will help you go forward.
I think this readings are connected with how much you listen to them. Kanjis with reading しょう、かん、けん readings are numerous. You listen to it all the time. You will build a kanji framework for them quickly.
If you looked from a "grammar" perspective, they would be the hardest. Most readings share kanji that look a lot alike to each other, but these are very very irregular.
But that is not what happened to me.
They are the easiest to remember.