Consume level-appropriate content on the side. At your stage, if you are an absolute beginner, that might be restricted to a textbook. But WK doesn’t recommend using it as your sole study resource. You need to reinforce what you see by seeking out material.
Invest the time to learning the basics about stroke order and try writing down a few Kanji to get the feel of it. Having tactile feedback helped me get acquainted with the Kanji/Vocab in a different way. Once you get the hang of it, you can look at even the most complicated Kanji and better see how it is constructed. It will also help get past the initial apprehension upon first seeing complicated Kanji (at least for me it did) because you can see its parts more clearly.
Sometimes when I was burnt out I sat and practiced writing some random words. It’s quite satisfying when you’ve drawn a nice looking Kanji, even if you’re unaware what it means.
I’m not sure what kind of logic you are expecting. Someone just decided long ago that certain sounds represent certain words. There is also no logic why the sound “ham” represents ham in English. You just have to use the mnemonics in WK to learn the words, listen to lots of audio resources and read stuff as Leebo said, and start associating the sounds with things in your mind.
Did you also go on to volume 2 of the RTK set? I haven’t done more than glance through volume 1 and read the amazon.com description for the second, but it looks like volume 2 is where he teaches the Japanese readings of the kanji. However, even with mnemonics, it’s still just a system for memorization.
As much as I wish I could just absorb Japanese and learn it effortlessly the way I did with my native language, that’s just not realistic. I think it’s generally recognized that young children’s brains are uniquely able to assimilate language. This doesn’t mean that if your parents didn’t use two languages with you from birth, you’re doomed. It just means that the rest of us have to work a lot harder to get to the same place.
As far as I know, rote memorization is unavoidable. RTK and Wanikani are different ways of making it a little less painful. Some people like to build vocab lists around a certain topic to study related words at the same time. Personally, I enjoy working through a textbook and workbook (currently using Genki) so that I have opportunities to use the words in reading, writing, listening, and speaking. If I can put the word to use, I’m more likely to remember it more easily.
This community has put together a great list of learning resources here: