- Install/uninstall does look much better now.

- Tabs are better for indentation than spaces, IMHO. You're replacing tabs with spaces, look at the following quote from your mod (highlight the leading spaces to see the difference):
<search for>
// Start the linktree off empty..
$context['linktree'] = array();
</search for>
<replace>
// Start the linktree off empty..not quite, have to insert forum
$context['linktree'] = array(array('url' => $scripturl . '?action=forum', 'name' => 'Forum - Index'));
</replace>
[li]Write comments properly, in the above example it should probably read:[/li]
// Start the linktree off empty... not quite, have to insert forum.
[li]Keep the indentation level of the code around the one you're inserting. Tabs will help you keep the indentation consistent, but in this case it's weird anyway, with the TinyPortal comment (which, BTW, is missing the period at the end) without indent and the next line with more indent than the line before your new code. Look at this from your mod:[/li]
<search for>
function template_main_above()
{
global $context, $settings, $options, $scripturl, $txt, $modSettings;
</search for>
<add after>
// TinyPortal
require_once('SSI.php');
loadtemplate('TPortalBlocks');
</add after>
should be
<add after>
// TinyPortal.
require_once('SSI.php');
loadtemplate('TPortalBlocks');
</add after>
[li]Make your comments unique, you use the "
// TinyPortal" one in several places. I've done this mistake myself in some mods.[/li]
[/list]
Again, very well done on the mod. I love how you explore the power of the theme engine. I hope you find the feedback useful.

A good read to refresh some stuff:
Coding Guidelines...