As a person studying Japanese since I was in medical school, I can tell you I definitely relate to your problem. I think, inevitably, what’s happening is related to the frequency of how often you see the kanji and are utilizing the mnemonics. I used to teach kiddos (my degree is in elementary education), and I found when my younger ones kept struggling to learn a concept, it was often because the way I was teaching it wasn’t sticking as their learning style didn’t match my teaching. So, what I would often do, is break them into groups and each day of the week was a different learning approach to the EXACT same information with a little new info sprinkled in. It’s called scaffolding and wow is it helpful to us as adults.
I say all this to say, what you might find the most beneficial, the thing that will likely help with retention the most, and the thing that will likely not only help with distinguishing the kanji but also sealing their meanings in for you, is to figure out what your particular learning style is, then modifying the studying done on here into your learning style. So, if you’re a kinesthetic learner (learn by writing, molding, shaping, etc.), as you do lessons, draw out the kanji at the exact time you study it and then review it. If you’re a verbal learner, you need to turn on the japanese pronunciations and not only repeat what they say out loud, but practice saying it as close to what they say as possible. If you’re a pure visual learner, then the method they have in place is perfect. Also, something that may likely help no matter your learning style: visualize an actual picture for each particular kanji, then in the notes section under each kanji’s meaning or pronunciation, simply write what that picture is (so for example, the “meet” kanji which is represented by the radicals for two, hat and private, could be two people meeting under a large hat in private discussing ways to take over the world; imagine them in a lab as they meet complete with gloves, crazy goggles etc. You then incorporate the onyomi and kunyomi readings for the word and you caption the picture world domination). This system is great for helping you distinguish these things as you incorporate the radicals, you create the image, and you scaffold the information all at once.
Finally, repetition. I cannot stress this enough as an adult. If you don’t regularly repeat this information, no matter how many things you do to remember it, you will forget it. We learn as adults almost purely through repetition as our brains are not near as plastic and ready to learn as when we we’re five. So, I’d highly recommend taking time every day to work through this information so that you’re touching it at least once a day. If you’re already doing that: great! If not, Japanese is an extremely difficult language to learn without constant reinforcement. It’s why I’m on my eighth year of studying it without having mastered more then 1000 kanji (joined this site a month ago thus why low level but I’ve been studying this language for years). I didn’t buy into the whole repetition thing and would often let weeks go by without any japanese being spoken, written or read. You absolutely cannot do that and expect to learn the language. It takes daily dedication, and if you wish to master it sooner, as frequently as you can dedicate if you’re not living in the country.
Is it work: absolutely. Will you want to quit sometimes: yep. But, as they warned when you started this program, it takes alot of work to learn a language when you don’t live there. So, you have to give it as much time as you can spare, and make it an enjoyable hobby that you’re willing to dedicate alot of time to. I motivate myself to keep learning it now by finding things to read that I can only read in Japanese. It makes the motivation continue daily because I have a reward that can only be reached by learning enough japanese to enjoy it.
Hope this helps!