You will need to correct the problem and any damage before timing the engine. The only way it can jump time is for the chain and/or the cam chain tensioner to be worn out or broken.
A leakdown test should be done to make sure the valves aren't bent.
Here is how to build and use a simple tester. http://www.motorcycleproject.com/motorcycle/text/leakdown.html
I haven't had time to draw up the 400, but I do have a cam timing drawing for the 360.
Rotate the motor over while watching the intake valve open and close. Go a little more until the T mark on the flywheel lines up with the pointer. This is TDC on the compression stroke. All of your lines should line up as shown in the drawing. You can verify your T mark by putting a straw down the spark plug hole. If the flywheel key has sheared, the T mark will not line up when the piston is all the way up on Top Dead Center.
Let me know if you have any questions on the timing, doing the leakdown test or any other problems you run into.
I appreciate the drawing. I must have set the dad gum thing 180 degrees out. If the 360 is anything like the 400 except for cam bolts placement. My cam timing mark splits tthe differance on the bolts. It is not next to the bolt as shown in the diagram. I will retry setting per your advise, pending a 400 image of the timing marks.
And I really like the leak down tester. Building one now. Thanks.
I've got some people looking for the 400 supplement info for me. It's the weekend so I can't access the manuals I have on my work computer. You can verify the cam position because the cam lobes should point down. IF the lobes are down and your mark is up, that is correct. If you are 180 off, if you rotate the motor another revolution, it would probably line up. You are just on the wrong stroke.
Did you have the sprocket off? Behind the sprocket are two lines horizontal lines that line up with the head. Lobes on the cam would need to be down.
Have you determined how/why it jumped time?
I do not have the correct information on that unit here at home. I'm going to opt out so someone can get you the correct info.