There's a 100 different ways to do this, but typically my favorite approach is to try to work the synonym into the same copy without seeming spammy.
For example, if my primary keyword is "GMO" and my very literal synonym is "Genetically Modified Organism" then I'd try to work both variations into the copy.

<title>GMO Dangers - Knowing the Risks of Genetically Modified Organisms</title>

Here's a great article that goes into depth about the advantages of incorporating multiple variants into your SEO targeting http://cognitiveseo.com/blog/5370/941-traffic-increase-exploiting-the-synonyms-seo-ranking-technique/

As many as you can get.

Stay consistent. Keep a schedule and build up your links over time. Don't rely too heavily on directory links. Remember that the harder a link is to get, the more valuable it usually is.

Most of the time you don't need to specify a base URL. The browser already knows this location. In some situations defining a base is helpful, such as mirrored sites when the URL used is not the same URL that is needed to resolve files.

Is your clients using a universal base tag that is the same across the entire site? I can't tell from the question, but this is a common situation that could potentially cause problems.

There's nothing inherently wrong with using a base tag. Most of the time, if you use it, you simply want to set it to the URL of the current page.That said, to avoid complications, the only time you really want to use the Base tag is when relative URLs wouldn't work without it.

You might want to test how the links on your site resolve and see if removing or modifying the base tag helps clear up your broken links.