I think you should be able to implement this easily. I haven't tested this out myself yet, but try these instructions (vb3.6.4-friendly):
Go to your Admin CP -> Style Manager -> Edit Templates (from the drop-down menu) -> Select "Header" and then click on the "Edit" button at the right.
There you will have your header vb code, and all you have to do is add a countdown timer javascript code where you wish. If you want to place it on top of the logo, be sure to use the <br /> code to separate a new line between the Countdown Timer code and your main forum logo.
Here's a link to the javascript Countdown Timer code:
http://www.hashemian.com/tools/javascript-countdown.htm
So, put that where you want it, and presto!
Let me know if you have any problems implementing this and i can give more details.
Cheers!