Re: Can I change the padding on top and have the logo not stretched?
These CSS rules apply here:
div#sioptions {padding:1em;}
div#sitelogo img {margin: 1em;}
You can override one or both by duplicating the lines and putting them in the Look and Feel Admin page's Custom CSS textarea (under the Miscellaneous tab), with values smaller than the current 1em.
On another note, I wonder why there is a table in the wikitext that seems to somehow include the site footer (the "powered by" line should be only .9em tall, not an h3 heading).
-- Gary