Hi @Jen Potter ,
Per my research, you could use some deleloper tools to find custom SharePoint CSS classes that you need to overwrite to change the colour of the hovering. For example .ms-welcome-hover and .ms-siteactions-hover are the welcome hover class obviously being the top bar for the page.
Then you could use the following code to change the hover color:
.ms-siteactions-hover
{
background-color:#000000;
color:#FFFFFF;
}
For Reference:
How to remove the Hover /or chage the hover color, when moving the mouse over the current username
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