Its very difficult to help because though this is a real problem for you it is only a theoretical problem for me since I have no knowledge of what is going on in your custom skin.
For solving all css problems you need to view the source of the rendered page to learn the relevant css class names from the markup. Then you can know what classes you are looking for in the .css files.
The links module renders as ul and li elements like this:
<ul class=linkitem>
<li class=linkitem><a ... the link</a></li>
<li class=linkaltitem><a...the link</a></li>
</ul>
So if you have css like this:
.linkitem{font-size: 80%;}
the ul will have font at 80% of full size for the page (see body{})
then because the li is nested inside the ul it will get font at 80% the size of the ul font and this is probably what happens in your skin.
it doesn't happen on the alternate rows because they have the linkaltitem class not linkitem.
So best solution is use specific sizes instead of percent or relative terms like smaller larger etc.
To find the css you may need to look in each of the .css files in your skin. This is probably in styletext.css but possibly somewhere else.
For mouseover issues you probably need to look for :hover in the css files to find the rule that causes this.
As of version 2.2.7.3, mojoportal no longer uses ExtJs tabs in Page Settings, Module Settings, Site Settings, but we use YUI TabView instead. So research skinning of YUI tabs to figure out rtl solutions for that.
Hope it helps,
Joe