Ok, there is a lot here so lets do the easy ones first then attack the others. The music track pop up box can be disabled by going to Options/Sound/enable onscreen music display and disabling it. As for you platform logos not displaying have you gone to Options/Image cache and refreshed platform images? The consoles logo appearing at the top is a feature of the theme, as is the wheel fading out. If you want totally full screen platform videos you will have to live with that ,or swap to a different view in the theme. I personal use the view below, not fullscreen but still a good size. Also I see in your final image of your file system that you have it setup rather strangely, you shouldn't have a folder called "customicons" launchbox will not no to look there all your clear logos should be in themename/images/platform/clearlogo or theme/images/playlist/clearlogo.
So you can try the suggestions here, and if you have any further issues or questions just post back I am more than happy to help.