The darkness is probably from two things, neither of which means you did anything wrong. 1) When in a large vessel, the beer will appear significantly darker than in a thin glass. 2) If your recipe uses LME, it makes it hard to get a truely straw or blond color out of a beer.
Definitely let it sit longer in secondary. Sounds like you might still have a decent bit of yeast in secondary, which should help in bulk conditioning, diminishing any young or off flavors. I'd say let it go at least another week or two. Let taste be your guide.