I just learned that I was reviewing the KanjiTransition deck completely wrong. What should I do from here?
The JP1K method is structured in a way that is a little hard to grasp for some people. Normally on an Anki card you only have one question and one answer, but the KanjiTransition deck and other JP1K-style decks out there have you review each card in multiple steps. If you suddenly realized that you didn't follow the instructions, e.g., recalled only meanings of words and didn't try to recall the readings, or graded yourself based on the readings and meanings, it clearly means that the JP1K method is not for you. Find another method of attaining kanji fluency.
There are several paths to take from here.
Switch to Ankidrone Starter Pack.
Abandon the idea of learning kanji and start learning words. When doing Ankidrone, try to learn each word as is, through the so-called brute force method. Memorize how the word is read and what it means.
This path is for people who failed to reach kanji fluency with JP1K but already learned more than half of the deck.
Do Kanjidamage+. Or RTK. Or any other isolated-kanji deck.
This is for people who couldn't stick with a JP1K deck at all and dropped it before the halfway point.
Start the deck over and try to stick to instructions. If you noticed your mistake very early on, try again but follow the instructions properly. This way you still have a chance to benefit from the JP1K method.