You'll have to edit the plugin file (Plugins > Plugin Editor > Peter's Date Countdown).

Do a search for "countdown_clock" (it should appear twice) and then replace some code above and below the two occurrences.

Find this piece of code:

// show the JavaScript countdown
else {
print "<script language=\"javascript\" src=\"" . $pdc_siteurl . "/" . $datecount_path . "datecountdownjava.php\"></script>\n";
if (!empty($pdc_message)) {
print "<p>$pdc_message</p>\n";
}
while ($i < $howmanydates) {
print "<p>\n";

And add the alignment and open the font tag on the last line:

print "<p align='center'><font size='4'>\n";

Then, close the font tag when the <p> tag is also closed later a bit further down.

Replace:
print "</p>\n";
++$i;
}

With:

print "</font></p>\n";
++$i;
}

This same code pattern appears again a bit earlier:

print "<p>\n";

$link = $importantdate[$i][7];
// show link if there is one
if ($link <> "") {
print "<a href=\"$link\">";
}

(add the font and centering stuff to that first line)

And then further down, close the font tag on the last line:

// close link if there is one
if ($link <> "") {
print "</a>";
}

print "</p>\n";


Also, I noticed that the real-time countdown doesn't work in your header but does for your footer.  To fix this behaviour, make two duplicate events, then call countdown_callit(1); in the header and countdown_callit(2); in the footer.