I’ve been doing the same thing with anime in order to pick up words that I hear but don’t understand, or new grammatical structures. I started when my grammatical knowledge was roughly at the N3 standard. It’s time-consuming and requires motivation (which is part of why I do it with anime – I’m having fun). As far as effectiveness goes… studying the grammar I came across in anime is probably the reason I was constantly bored while going through the grammar lessons in Tobira, which is an intermediate N3-low N2 textbook. I had come across almost everything already. In my opinion, it’s potentially very effective, and anything to which you attach a strong emotional response will likely be easier to recall later. However, I don’t know how much you’ll retain with a 50% comprehension rate, because I don’t know if the story still makes sense to you. I’m not saying it won’t be effective… I’ve just never tried that. I know for one that when I watch anime with subtitles, even if my listening ability is such that I understand most of the Japanese without looking at the subtitles, I won’t retain much unless I stop the video and look up the word that’s confusing me. Anything I don’t focus on and figure out doesn’t stick.
If you want to see whether or not parsing sentences you find difficult might help you, but possibly without having to do the work yourself… try this thread:
It’s the entire reason I’m on the WK forums in the first place: I was roped in to help explain things to people who wanted to try their hand at learning Japanese by tackling a manga even though many of them didn’t quite have the grammatical knowledge required to understand it easily at the time. My way of handling translation when I took a sentence was to supply a word-for-word grammatical breakdown before providing a readable translation. This post is an example:
Another example, from the NHK Easy News thread this time:
I’ll leave you to take a look and ask yourself whether you feel compiling all that information and absorbing it yourself would help you retain new grammar and vocabulary. I think it can, but it depends on what suits you.