crank shaft and cam shafts are out of alignment
 

The crank shaft and cam shafts are out of alignment.

Where do I start to put it all back in the correct positions?

So far I have moved the crank shaft so that the number one cylender is all the way up.

What would be the next move? How to I ensure the right side (left when facing) cam is in the correct position?

Sorry guys I'm lost.

The timing chain has colored links on them. You just line up the colored links with the indicator on the sprocket.

https://www.nicoclub.com/service-man...F2010%2FEM.pdf

Scroll to page EM-54 and start there.

So the number one cylender lobes need to be stright and the number one cyclender needs to be all the way to the top? I can turn my crank shaft so that the number one cylender is all the way up but the number cylender one lobes are all the way down (valves open), this is where I think I'm off. Please clearify if you understand, thanks!

You don't need to worry about cylinder positions or valve lobes. This is all accounted for already. Just line up the alignment marks with the colored chain links, and its set. The link I posted above includes further detail. EM-61 is where it goes specifically into timing the engine with installation of the chains. On one side you align with a dot and on the other side with a oval, something along those lines, I havent done it in years. But its all in the service manual section.

Sorry guys, I guess I didn't explain very well. The crank was turned after the main timing chain was pulled. I trying to line the top dead center (number one cylinder at the top) back to the exhaust lobe positions of the of the number one cylinder. I'm thinking the number one cylinder needs to be all the up and the exhaust cam lob needs to be in the position as shown in EM-58 26.b. manual. Would this be correct? Thanks for any reply.