Nmidia - If you can figure out how to port the shoutbox from vBindex, then there's no problem here. You may want to check with them though as they may require a copyright notice or something like that since you're using their script. I will be making a shoutbox as an add-on for this soon... I'm working on getting vbadvanced.com up (hopefully by next week) where we will provide support for this scripts, hacks, and other stuff.
Casparian - I'm not quite sure I know what you mean by the spaces and comments in the who's online list... As far as the colors, I'm assuming that you're acomplishing that through the "Username HTML Markup" option, right? I'll be sure that's added in the next version. I don't think listing the online users in rows will ever be the default way it's done since that could cause that box to become huge, but I could probably release a hack for it once vbadvanced.com is up and running.
As for the "Unknown Location" on the Who's Online page, there is a fairly easy way to fix that. I'll have to find the code and post it when I have more time... Just an FYI though, only admin's will see the "Unknown Location" text - regular members will just see that they are on the forum's index page.

To make your header look like your forum header, you will need to modify your index_header and index_footer templates to match your forum ones.
As for moving the blocks around, those can all be modified in the index template. Everything is well commented, so as long as you know at least a little HTML then it shouldn't be hard at all to move them where you wish.
Rids - I think the problem with the icons is that it's pulling them from the icon cache rather than the actual path that's in the database... At least that's the only thing I can figure since everything else does seem to be correct. Try modifying your thumbsup icon, just save it in the icon manager without making any changes, and let me know if that makes a difference.
I may need to throw some code in there to update the icon cache after the image paths are modified...