Welcome to the forum
All the head bolts should be the same length.
Yes in 1999 the Vulcan 3.0l got longer head bolts, but all are the same length, just longer than 1998 and earlier.
Your engine is a 2001 3.0l so will use the longer bolts
But it is very easy to tell which head bolts are correct
In 1998 and earlier the threads in the block for the head bolts came right to the surface of the block.
In 1999 the threads are recessed in the block
Go here, about 3/4 of the way down the page you will see picture of recessed threads: Ford Ranger II 3.0 liter Engines
Recessed thread blocks use the longer bolts, heads are exactly the same
After head is in place
Tighten each head bolt to 37ft/lb in correct sequence
Then loosen each head bolt, in sequence, 1 full turn(360deg)
Now tighten each head bolt to 22ft/lb, in sequence
Then tighten each head bolt 90deg, in sequence
Then tighten each head bolt 90deg, in sequence again
Make sure threads are cleaned out, oil a head bolt and with head removed run the bolt down all the way, as far as it will go, no need to torque it just make sure if goes down smoothly.
If the same bolt broke twice then you could have bad threads in that hole, may need to run a tap down it to clean it out
Also test your torque wrench
Google: testing torque wrench with a vise
I had one that lost calibration and caused me some problems