On and Kun Yomi Readings

There is a Userscript that changes Onyomi readings to Katakana (not sure if it’s exactly what you’re looking for but might be worth a look) ([Userscript] WaniKani Katakana Madness) as well as [Userscript] ConfusionGuesser which can let you know whether you got the kun and on mixed up when you get a review wrong (Not sure if that’s what you’re looking for either, but if you do decide to get it, make sure to check out the settings and change it so you can easily recognise the colours)
Some users also write down their lessons by hand, so you could do that and separate onyomi and kunyomi, or use different colours if that’s how you learn.
Stroke order is an important part of writing kanji, it really helps with figuring out which kanji is which with handwritten kanji as well, and can help with other things like radical learning and searching for kanji etc. but it’s only important if you are writing the kanji, if you don’t write the kanji, then it’s not super important (as well as that will make it super hard to remember without the practice of using it). There are heaps of threads in the forums about writing kanji and the benefits, uses, methods, need, etc.
So it really depends on what you’re doing and your goals for your Japanese. Maybe trial a few things and if they don’t work then it’s not a problem, everyone is different and learns in different ways (i.e. for me, i usually have to do practical things which engage multiple senses to remember things well).