Also, a way to change the color when hovering over a link?

To change the hover color for basic links, use this:

a:hover {
	color: hotpink;
}

Change the color name to a color code of your choice:
http://automattic.github.com/Iris/

Note that some elements have more specific rules for hover color, and in those cases you would need to add specific rules to override each one as you find them.

Is there a way to permanently change the default font color from grey to black?

Sure. There are a bunch of selectors in the Fresh and Clean theme that set various elements to different gray values. Here's a list I would use to turn them to black:

body,
.entry-content,
.widget-title,
.widget-title a,
#access a,
#access ul ul a,
.featured .entry-summary,
.sticky-label,
body.single .entry-title,
body.page .entry-title,
body.attachment .entry-title,
.archive-title,
.entry-meta,
.featured .more-link a,
.page-link a,
#site-info,
#site-info a {
	color:#000000;
}

Is there a way to permanently change the default font color from grey to black?
Also, a way to change the color when hovering over a link?

Thank you!