Having messed around with this kind of thing recently, I've found the really confusing bits can (sometimes) be cleared up by trying to figure out a bit about the underlying sentence structure. I've been using
https://www.romajidesu.com/translator to break down the original sentence and then looking up the words themselves to try and figure out what's going on. Particularly when trying to figure out the subject/object/etc of the sentence - if the MTL is confused about that it can throw the whole translation out. And my /god/, the verbs, they're /such/ a massive headache given how many forms there are, and how much extra information is packed into them. Oh, and half the time I find myself working through the broken down sentences backwards? Like, "oh, hey, starting from the end and working back it kind of makes sense . . ." Maybe my native English speaking brain is just messed up?
Unfortunately, no matter how hard you try there are things that just end up not making much sense - nothing much you can do about it short of asking someone who knows the language better than the machines do . . .
Honestly, how anyone can learn Japanese without growing up with it is beyond me. Mad props to all the non-native Japanese speakers out there - you're all /gods/, I swear . . .