Theres a couple ways to do it. You can adjust the image itself so it aligns with the nav more by using photoshop (or whichever program you used to edit the image).
Another (quicker) way is to add the following code to your .header-image .site-title > a
on line 1232 –
position: relative;
top: 20px;
It should look like this in the end
.header-image .site-title > a {
background-size: contain !important;
display: block;
height: 60px;
text-indent: -9999px;
position: relative;
top: 20px;
}