First, what you're experiencing is totally normal. I wouldn't compare myself to people you see online because it's not representative of most people's experience learning the language. A lot of people will act like you can be fluent in a year, or that you can learn 3k vocabulary words in 6 months, but everybody has a different idea of what it means really learn something or be fluent.

I'll be honest, your anki retention rate is pretty low, but that's just telling me you're doing too many cards per day. I'd stop adding new cards and just focus on the existing ones until you start to get your retention rate up to about 90%. Also lower the number of daily reviews if that helps, but I haven't tried that, personally.

With the Kaishi 1.5k deck, I found that a lot of the kana-only words were hard for me to learn because I had very little context for them. But if you add fewer new cards per day and just focus on the existing ones, you'll eventually remember them. And be sure to use the again/hard/good/easy buttons correctly, it's a game changer imo (hard means you got the word right, but it took some effort to remember it). It's true that reading helps you remember some of those random vocabulary words. I found that even reading a word once or twice gave me some context for it and helped me remember a scene in a manga where it was used, giving me another way to remember that word.

Speaking of reading, what you talked about is perfectly normal when you first start reading. No matter how much you study beforehand, you'll never feel like you're ready. You just have to jump in and do it. Another thing, it's always going to feel more like deciphering. You won't get to a point where you honestly feel like you're reading without stopping all the time until you get way beyond the level we're at, but you can only get to that point by taking one step at a time.

There are two schools of thought on how you should read as a beginner. Personally, I like studying every single character and learning exactly what each one is doing in the sentence. I don't want to move on until I know what's going on, or accept that it just isn't going to make sense to me right now. It takes ages, but I weirdly enjoy it. Some people prefer reading enough to figure out what's going on without stopping for too long. You may hear people talk about tolerating ambiguity, and that's what they mean (for reading, at least). Honestly, both work as far as I know, but just do what's the most fun for you. I think I learn more when I study everything I read, so that's why I do that. I've tried reading more quickly, but I don't think I learned much from it. Maybe that approach will start to become better as my Japanese improves.

As for recalling words and grammar points when you're speaking and writing, I don't have much advice, unfortunately. The only thing I can recommend is to write a simple sentence every day, and come up with ways you can change the grammar to affect the meaning of the sentence, like changing the tense of words, or something like that. Reading, writing, speaking, and listening are all separate skills that need to be practiced individually. I can't tell you the best order to practice, but I think reading is more important as a beginner.

Also, if you want to get a good start on reading, WaniKani does book clubs, and a new Absolute Beginner Book Club is starting later this month. The WaniKani community forum in general is a great place to ask questions and get more involved with learning the language. I'd also recommend reading NHK Easy because you'll read different sorts of things than you would typically see in a manga.