re: the alignment...
go through the files both in the "simple_zen" templates folder, and the "default_template" templates folder, and especially on the tpl_(problempage) and the tpl_main_page, and look for instances of the following :
Code:
<br class="clearBoth" /> OR <br style="clear:both;" />
change them to
Code:
<div class="clearBoth" />
that will fix a lot of little layout problems.
also make sure that any IE hacks used in the stylesheet use the right syntax.
as far as font sizes, see what divs the fonts in question are located in, or what styles are being applied, and then check your stylesheet to make changes to those particular ones.