Changing your file structure will not destroy your search engine rankings or your google pagerank if you do it properly. If you 301 redirect your pages to the new location then you will normally see a slight drop in search rankings for a couple weeks but they will come back. I move pages and change my linking structure all the time and my rankings always come back.
Changing the content on your site is another story. If you go messing around with your title tag, h1 & h2 tags, your interlinking, etc, then do as Dominique says and move slowly. Make minor changes and wait to see how it affects your rankings. If you change the content up completely so its no longer related to the search term your ranking for then be prepared to completely lose that ranking unless you have a ridiculous amount of quality backlinks with those terms in the anchor text. An example of this would be if you search google for the term “click here” you will see adobe reader ranked number one. Its completely unrelated to the term and doesn’t even mention “click here” anywhere on the page but everyone links to it with some phrase such as “click here to download adobe reader.”
If you want to install wordpress as a cms for the site, go for it. Just make sure you 301 redirect the old links to the new ones and you will be fine. You also have the option to set your permalinks so that they match the old URL’s if your worried about it.
I wouldn’t change your content completely though. If you have good rankings for this site, don’t risk it. Just set up a new site and use that site as link juice for your new one.