I am writing a text and I want to say:
With the passing of time, I have understood what he wanted to say.
I have written:
Is my sentence completely wrong?
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I think your sentence is great. The only real choice left here is the tone you want to adopt. You chose a polite form of speech with lots of glue words, which conveys a certain signal. In contrast, if you chose a bit more blunt form, it can convey a stronger conviction, with more emphasis on "I".
Also, since your fluency is already pretty high, I shall point out it out, even though it is more of a nit, that three "が" in one sentence feels a little too repetitive. I'd think 彼の言いたかったことが flows a little better.
Finally, a few other variants for your consideration: