vBulletin 3 is fully XHTML complient or as close as possible, and its fairly well written code IMO. The generic Shell is a generic shell, if you want to effect mosdt o the forums you should be editing the header and footer templates. However, this is NOT the place for discussion of templates, that is what vBulletintemplates is for, and No you cannot execute phpcode in the templates you need to either hack this into a signle file or multiple files OR use the phpinclude_start / end templates.
It is not CSS-compliant, however, as I found out. Unfortunately the fix is very simple but I am doubtful if it would be made official: underscores are not allowed in CSS class names.