It's a very useful hack and idea is very nice either, congratulations!
Just one tiny concern in my side: You (and your members) will use the vbcode for a few messages only, however the java code in the header will be loaded with every page (not just for messages either, with even in calender or user CP pages) in your board.
Maybe it could be nice to check the message inside "showthread.php" before displayed whether vbcode exits or not and if it exits, make the neccessary parsing inside the same script again.
This method both saves you from the java header and it could also be possible to count down according to thread reader's local time

Even if you wouldnt regard this method, adding the java code to a relevant template (which is related to thread displaying only) can help to get rid of it for at least unrelevant pages. Just my 0.2 cents.
Congratulations again!
Logician