For the purposes of estimation, just use the total number of items you’ve learned (minus the grammar points.) You’ll have “forgotten” some, and know some not on the list.
As others have mentioned, the key issue is two questions:
- What is a word? Do conjugations count? Do compound words count? Do particles or counters count? Do interjections count?
- What is knowing a word? Is knowing being able to use it in a sentence? Is it being able to recall the full dictionary definition? Is it being able to read it from the kanji? Is it being able to know it’s meaning from the context a sentence? Is it being able to use it correctly in a sentence, maybe as part of a phrase, but not actually know it’s true meaning? Is it being able to use it in a game of Scrabble?
These questions are entirely subjective, and it’s easy to inflate or deflated perceived word counts based on your definitions.
The more you progress in a language the harder it will be to precisely state how many words you know. You can estimate, but only estimate. You’ll know a lot of words just based on the context they are used in.
Additionally, it’ll become apparent that words are not isolated units of information, but pull along with them context, patterns and nuance. So it’s fine to count phrases too as words.