Tamiyo's Journal and the Legend Rule
Yes, that's perfectly legal, assuming that you started with 6 clue tokens. Hard to point to a specific rule saying so, but there's 2 things to keep in mind:

1 - The legend rule, which you quoted, doesn't say anything about restrictions on which of the duplicates you have to choose, so there's no reason you can't choose the tapped one to get rid of and the untapped one to keep.

2 - Tamiyo's Journal doesn't care where the clue tokens came from; it doesn't have to be the same tokens that it created.

Of course, as described, you will get no benefit from this: you'll have just wasted 3 clue tokens and 5 mana. But it could be good with various combinations.