Terms:

Before getting too far, let's be sure you understand the language used below.  The following are a few terms you should understand.

#1TDC means the #1 piston, which is the front piston on the right side of the engine is at the very top of it's stroke after the exhaust stroke.  There is an indicator on the crank pulley that will line up with the marker on the timing cover when the engine is at #1TDC.  Fig 1, below shows the crank in this position.
Safe mode means the pistons are all below the deck, or top surface, of the engine block.  This is important if you need to put the cams into the correct position while the heads are on the block.  If the pistons are not in this position, there is risk of damaging valves while turning the cams.

Preparation:

The first step is to mark the various indicators with something that is easily visible.  I used a gold paint pen, but a bright nail polish works just as well.

With the heads off the engine, make a mark on the crank sensor ring at 12:00 when the crank is at #1TDC, and at 12:00 when it is in safe mode. Put the engine in safe mode by turning the crank 45° counterclockwise from #1TDC.  These marks leave no doubt as to what position the pistons are in when either of the marks is pointing straight up. Take your chains, fold them in half (you can look for the slightly darker links if you want) and mark the end links. 

If the heads are on the engine, you can put the engine at #1TDC by rotating the crank until the pointer on the crank pulley points toward the #1TDC indicator on the timing cover (if it were in place), the keyway is at 10:30 (315°), and the mark(s) on the crank gear(s) are pointing straight downward toward 6:00 (180°).

Set the timing:

Put the engine in safe mode, adjust the cams to where they need to be according to your timing diagram (Chilton's, Haynes, Ford, or Fig 1, below), then put the engine to #1TDC. At this point, the lines on the two smaller crank gears will point to 6:00. Set the left side first. Pull the crank gear off, drop it in the chain so the marked link is lined up with the line on the gear. Put the gear back on the crank and pull the straight side of the chain tight. Wrap it over the cam gear, install the tensioner arm and tensioner (don't release the pins yet) and, using a 3/8" breaker bar, adjust the cam timing mark to line up with the other mark on the chain. The straight side of the chain must be tight when they're lined up. Make sure the other end of the chain didn't slip. If they're lined up, pull the tensioner pin. Repeat the process on the other side. If the cranks gears are in two pieces, make sure the crank gears are installed correctly with the shoulders facing each other.  Once both sides are done, double check all the alignment marks to be sure everything is in the correct position.  Use the balancer pulley on the crank to manually turn the engine over. Make two revolutions on the crank pulley.  If you are making piston to valve contact, you won't be able to turn it over. Take it all apart and try again.  If you can go all the way, you're not making piston/valve contact. Congratulations!  You've set the timing and are ready to move on.

A few notes:

When putting the crank gear(s) and trigger wheel on the crank, pay attention to their orientation.  There have been different styles of crank gears and trigger wheels over the years, and they need to go on the same way they came off.  If not, binding of the crank and/or misalignment of the timing chains will occur.

Before rotating the engine, be absolutely sure the timing marks are where they should be.  There have been cases where a chain can be off by one link and still not make contact.  The car can run well from a drivability standpoint, but will be down considerably down on power.

1, 3, and 6: Marks on chain

2, 4, and 5:  Marks on gears

7:  Keyway on crank

8:  #1 TDC position at 10:30 or 315°

The mark I made on the crank pickup ring to signify #1TDC.  The keyway will be at 315°, or some people like to call it 10:30.  You should have another mark (not shown here) 45° clockwise from the #1TDC mark that will indicate safe mode.

Crank gears from below.  Notice the line on the gear is pointing down at 6:00.  The gold painted links are lined up with those marks.

Driver side cam gear.  Notice the line just before 12:00 (with the gasket plane of the head referencing horizontal) and the paint mark are lined up.  The timing mark is the recessed mark, not the protruding one.

The marked links of the chain need to line up with the straight side of the timing chain pulled tight.

The passenger side cam gear with the timing set.

The passenger side timing chain fully assembled.

All finished with timing.  By hand, rotate the crank with the balancer pulley to check for interference.  If there is any, take it apart and start over.