As the editor is primarily an HTML editor, "code" like this {user id="input:uid"}, which is not HTML code, is treated as text and processed accordingly. JCE does have an option to attempt to protect shortcode like this, but it does not work very well in multi-line scenarios llike yours.

In addition, the combination of script and link elements, which must also be treated slightly differently to regular HTML for security reasons, complicates things.

The best way to deal with this is to tell the editor that this is all custom xml code, and to therefore ignore it. To do this:

1. In Editor Profiles -> Editor Parameters -> Advanced, in the Code Blocks section, set:
   1. Enable Code Blocks to Yes
   2. Allow Javascript to Yes
   3. Allow CSS to Yes
   4. Allow Custom XML to Yes
2. In the editor, select XML from the Format list (the last item) to create an XML Code Block.
3. In this code block, create a custom XML container, eg: <custom></custom> and paste you code into this container.
4. Press SHIFT + ENTER to exit the block

This will then protect your code, but the browser will ignore the <custom> tag in the front-end.