Multi-Quote is not currently available. vBulletin does not provide a generic multi-quote for use in multiple content-types. See blog comments in the vBulletin Blogs add-on; it doesn't have multi-quote either. Therefore separate multi-quote functions must be created for each content-type. This is a separate regression and not related to any display issue.
If color schemes do not match your custom styles, you must alter the provided stylevars for comment headers and contents. This is standard. I do not see any problems with the color scheme on the Default Style.
View, Options, and Moderator Tools drop-downs were broken because the editor was broken -- if you recall you have a mixed content warning that is sometimes blocking the toolbar from loading. When there is no editor, I don't see any issues with drop-downs. I would recommend figuring out the source of your mixed content woes.
I don't see any issues with autolinks or URL BB-Codes.