red-i: Have you looked at this
page at Nicky's? It cleared up a few of my questions. The page is outdated and there may be newer programs that can be used, but the basic A/V sync issues are well explained.
As for your wma/wmv experience - can you run the file through Vdub - filter and rotate - save to .avi - then encode to .wmv? I've no experience with encoding to Windows Media Player. (yet)