One of the things I found that helped me the most in the beginning was exercises to go along with the new grammar I was learning. In my case, I used Genki and its workbook, which started from square 1 in teaching things like これはペンです. Have you done much in terms of practice exercises? That along with beginner’s reading practice can really provide you with a good foundation. In my case, again, the beginner’s level reading passages in Genki helped me practice and improve in that regard.
Are you looking for new resources in general? Or just some tips? I know not everyone is a textbook learner, so that depends on you, but I do think they have a lot to offer in terms of practice for someone at your level. For a slightly different, WK-like approach, there’s the site Bunpro for learning grammar (which is paid, although there’s a free version as well). There also are beginner’s level graded readers that offer good practice, though those can be more expensive.
Tae Kim’s site also has lots of practice sentences, and he begins from square 1 in terms of grammar, as well. His sentence translations are sometimes done more literally, which can make it easier to see why the Japanese constructs used resulted in that particular meaning in English.
It sounds like overall, you need to increase your input. You may not be seeing enough sentences or enough variety in them to be able to improve your comprehension right now.