I'd find the d/l links on the left much better than centered (the last line of code is very often short and usually not indented much or at all, so putting the link on the left usually makes it closer to the actual code content, making it clearer what it is for). As for the gap, I think this would fix that for CSS-enabled browsers:

.code { margin-bottom: 0; }
.embed_code_dl { margin-top: 0; }
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Updated CSS that works right now in user-specified CSS is:

tt.code { margin-bottom: 0; }
p { margin-bottom: 0; }
div.embed_code_dl { margin-top: 0; text-align: left; }
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"tt.code" is required because that is what the site CSS uses so ".code" isn't considered specific enough to override. The "p" is needed when "auto" code wrapping is turned on because the HTML produced is <p><tt class="code">...</tt></p><div class="embed_code_od">....

So I'd change the HTML output to <p class="code"><tt class="code>... and change the on-site CSS to use .code instead of tt.code, something like:

.code { margin-bottom: 0; display: block; }
.embed_code_dl {
  font-size: smaller;
  text-align: left;
  display: block;
  margin-top: 0;
}
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