This may be a bad question, since it's not very specific and I am very long winded.
I've studied Japanese on and off 7 years, though my level is very low and I never had much immersion besides a year of language exchange once a week and 2 weeks of travel.
I find I have a lot of trouble getting a true sense of the meaning of words which become the elements of enormous numbers of grammatical phrases. Even if I believe I know at least some meaning of the words and particles in a phrase, I can't intuit the complete meaning. To me it always ends up seeming like these grammatical phrases are more than the sum of their parts.
In my head the word ところ means place. Because some Pimsleur audiobook drilled it into me that I should say わたしのところ、あなたのところ 7 years ago.
But I know another meaning of ところ。ところで - By the way. I have it memorized, I'm not confused when I hear it.
And there's ところから - because of...
にしたところで - even for, also.
Is this a different ところ which is just a homophone? What's the connection? It starts to have a meaning like こと and の.
ように can mean like, as, or in order to. Is it the same word, or is it a homophone?
How can I determine the essential meanings of these important words? I have the Japan Times series of Grammar books, Beginner, Intermediate and Advanced. Certain particles and words appear again and again, but I don't have a sense for why in composite they form the meanings that they do. So I find myself lost when I come across one I don't know, and surprised when I learn the real meaning of it, and rather than happy I found it, feel very lost. I'm also vulnerable to the trap of trying to assign an English word to a Japanese word. いつのまにか - before I knew it. None of the parts match the English, but I can't understand the meaning and context otherwise. I don't know why いつのまにか means what it does, even though of course I know 何時、間、の、に、か individually in one or more meanings.
To make this question answerable, I guess I want to know A: are these basic elements of Japanese grammar homophones that have nothing to do with each other and B: If not is there a good guide for me to not just find an individual meaning of these words in terms of their usage in grammatical structures, but a more holistic approach which tries to explain why and how they combine into this wide set of usages. I was sold on the Japan Times Grammar books as a bible of Japanese grammar for learners, and they are good, but I end up with a long list of specific examples and their english counterparts, rather than an explanation that would help me intuit their usage, let alone build up those more nuanced and complex meanings myself.