First question... to get rid of those function links, you'll have to edit the CGI files. Those links are in Ultimate.cgi, Forumdisplay.cgi, ubbmisc.cgi (I think), ubb_library2.pl, and maybe ubblibrary.pl too. The links are kinda spread out in various places throughout each file. Search those files for the names of those links, and you should be able to find their code. Just remove the code for all five links from all of those files and it will be gone.
For the second question, you should make a 1x1 transparent image and use it as your logo image in the control panel. Then specify your top logo bar in the Header field along with the rest of your page layout.
---Skorpion
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strategery.
dignitude.
lockbox.