Not really enough information is provided in your post to help you very much.One thought -- if you didn't find the real "top dead center" and instead found the one that is two valve cycles off from the real one then your valves can knock when you first run the bike.
Gotta watch them valves open and close to pick the top (use a soda straw) of the compression stroke (all valves closed and slack) and stop on top dead center of just that one alignment point to do the valves.Verslagen is referring to the Clymer's book error that tells you to rotate the crank backwards to the way you should really do it.
Crank always should rotate the same way your rear wheel rotates.
Your Clymer's book should be notated with the correct rotation direction.
Take the time to fix IN YOUR COPY OF CLYMERS all the known Clymers errors right now -- saves you endless trouble later on.
Here is your list of Clymer's errors that need fixing.
http://suzukisavage.com/cgi-bin/YaBB.pl?board=tech;action=display;num=1119775997