Putting the timing chain back on correctly

The cam will have a dowel pin in the end of it. that pin goes into the sprocket. The crank has a keyway in it for the sprockt to go on.the dots face each other. the cam dot aims down, the crank dot aims up. assuming you had the number 1 piston at top dead center you will want the cam set where both valves are closed. You want it set top dead center compression stroke. then all will be good.
 
Yes, turn the crank until the #1 piston is clear at the top of it's stroke. But you MUST be sure it's on TDC of the compression stroke, not the exhaust stroke. If you can view the rocker arms, looking at them will help.
 
It's easy. Remove the spark plug for the #1 cylinder and stick some type of probing tool in there (screwdriver works, but be careful) and turn the crank. The #1 cylinder will push the screwdriver up. As it is, watch the exhaust valve rocker to make sure it's not being pushed down. If it is, your on the exhaust stroke. But if the rocker arm doesn't move while the piston is moving up, it's on the compression stroke. This is where you want it.
It's kind of a cheap way to do it, but it works.