Since you’re using romaji, one tip I have for typing つ vs っ is that, rather than typing “xtsu” to get the small つ, you can actually type a double consonant. Of course, I’m not sure if you are already doing this, but in case you aren’t, or if anyone else sees this thread, I’ll explain down below.
Let’s take the word 切手, for example. The hiragana spelling is きって. On a romaji keyboard, you could type “ki xtsu te” into WanKani. BUT, you could also type “kitte.” And this is how the word actually sounds! Plus, there is no way to accidentally write a big つ. Typing that double consonant (tt) automatically adds a small っ.
Also, I know you already said you read some Tofugu articles. If you haven’t read their guide on Japanese pronunciation, you may want to do that. Alternately, finding a video on it may be more helpful tbh, as their article is decent but not necessarily my favorite.
If you haven’t heard of mora before, that may also be something to look into. This might help you understand long vowels, aka what you referred to as the “U” extension. Essentially, mora refers to the “beats” in a word. Each mora takes the same amount of time to pronounce. In the word さようなら for example, there are 5 moras, one for each character. You’ll notice the long vowel, よう. This still takes up 2 beats. It is distinct from さよなら, which only has 4 beats. The “U” extension isn’t a random spelling thing, it genuinely changes how the words sounds by changing the length of time you hold the vowel. I find that practicing words by slowly saying them out loud with the right rhythm helps me remember whether a word has a long vowel.
As for additional rules for writing, there isn’t anything that I can immediately think of, at least as it pertains to spelling. If you have any other specific issues you often experience or specific questions maybe you could list them out and folks here can try to explain? I hope this makes sense lol!