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For the logo size, you'll have to edit themes/default/theme.html. Look for the code containing the <{$xoops_imgurl}>logo.gif or something similar.
For the menu, do a search for the myMenu or iMenu module. That lets you create manu blocks on the fly. You can turn the menu itms of modules off in the modules administration (system admin -> modules), but setting the module weight to '0', this hides the modules in the mainmenu.
Herko