Main Menu (header) links hover area issue – how do I make them smaller?

I’ve got a page that is using a portfolio masonry grid with sort filter links in place. We are using the filter links as the sub-nav of the page. When I place the “sub-nav” where my designer wants it – the links don’t work.
It appears that the Main menu (header) link hover area is covering my filter links and blocking them from working.
When I set it up so the filter links are above the header elements (z-index), the whole grid is in front, and my header ends up behind it when I scroll. Therefore, I have to leave the header (main menu) on the top layer.
How do I make the link hover area smaller for the header area (main menu)?