i know its been a while and you probably already figured this out but here goes anyway.....
set the crank timing mark to TDC 0deg on the timing mark on the case.
set the cam gear so that #1 cylinder valves are closed.
once you have this set correctly when you install the chain it has 2 blue links, they should align up with the timing marks on the gears.
Note: on distributor engines (older style) you will have to align the oil pump shaft slot and then insert the distributor so that it sets up aligning with the #1 plug wire journal on the cap. (this is old school stuff though) ;o)
this is best explanation i can derrive from the manual
its pretty straight forward when it comes to setting engine timing.
just remember 3 things
1- set crank to 0 deg on the mark on the timing cover
2- set cam to compression stroke for #1 cylinder
3- align marked links on chain to marks on gears
these 3 rules should get you a good timing setting to start with, if it has electronic ignition with no distributor then the ECU will take care of the timing adjustments or you can make incremental adjustments in the laptop diagnostic program. If it has a distributor then you can use a timing light and set the timing to the desired setting of 0 deg @ 700 rpm.