The presence of a Villain that doesn't physically appear until near the end of the series.

In the series I'm planning out I've encountered a problem, the main villain of the over-arching plot only physically appears near the end of the series. This Villain, over the series, is mentioned and talked about throughout the story, but I feel like I haven't done enough to make him have a presence throughout. I especially feel his presence is weakened as I have many secondary-villains planned throughout the series.

One idea I implemented was that the protagonist forms a mental connection with the antagonist after taking a weapon forged by the antagonist in question, as soon as the antagonist realises the connection exists, he utilises it to taunt, scare and hurt the protagonist.

Any other suggestions?