Send box (when clicking on send) displaying underneath comment box

Those modules are loaded in iFrames, and when they overlap, weird things can happen. You can try the following, but I can't guarantee it will work. In your template's CSS file, try adding the following style, which should indicate that the Like/Send modules should be 'above' any other modules, even when they expand:
Keep us posted, and hope that helps,
Alex

There's no easy way to add text above the Content Plugin widgets. They behave differently than the modules, and so it's a little more difficult to have a pre and post-text simply because we'd have to have parameters for all the different types of views and configurations, whereas the modules are generally pretty specific to an area of the site.

As for the ordering of the Like & Comments, you'll have to make a minor modification to our code to make that happen. Honestly, after looking at it, I agree that the Like box should come above the comments, at least at the bottom of the page. The change below will also re-order the widgets when at the top of a page, but don't think many/any people put the comments on top of an article. Anyways, here's the change:
In the /plugins/content/jfbccontent.php file, at line 148, you'll see an 'if' statement with a big block of text until line 161 inside { and }. Below that is another big 'if' block. Just swap the order of these two sections and it will swap the order of the Like & Comments.

Hope that's clear, but if not, just let us know. I put an issue in our tracker to re-order these as well, as I think that's better overall.. but we'll have to discuss internally, so no guarantees that this will be in the next release.

Keep us posted on your results, and good luck,
Alex

To add a space, there's a few easy options. The best/easiest is likely to simply add the following to your stylesheet:
.jfbclike {
margin-bottom:10px;
}

Another alternative is, in the same file you modified before, in the same section, you'll see a line of code that starts with $likeText = "{JFBCLike ... and goes on for a few lines. At the end of this, simply add a line break, so the line should end like: '}<br/>';

As for the comments themselves, they are stored on Facebook's servers. Each comment is associated with a specific URL on your page. When using the JFBCComments module, we will use whatever the current URL is (unless a specific one is specified in the parameters). With the content plugin though, we know we're in an article, so we try to determine the canonical URL for that article (which will work from blog views, section views, and the article itself). Generally, these the module and content plugin should create the same URL, but there are cases (depending on the configuration of your site), where they're different.

If you really need to save a few comments, you may have to enable the 'old' module on just those pages and tell the content plugin to exclude those articles. Then, going forward, use the content plugin on all new articles. Unfortunately, Facebook doesn't have a way to migrate comments from one URL to another.

Good luck,
Alex