1. Go to Administration, then Modules, then under the colum functions you can disable enable them and whether they show in the links block you are talking about.

2. I'm no great wizz at this questions but that is simply the images the block is made out of try going in your smartDark folder then images and looking for the image file which shows the side of the block then using Photoshop you could change the colour of the edge.. pretty simple.

3. You need to look in your smartDark folder again and open up header.html where it shows the logo.gif or logo.jpg change the width and height values to whatever your image size is or put them at 100%.

If you want anymore help don't hesitate to PM me.