You can find the older threads on this site (nhtoc) by searching title only using "Production numbers":
http://www.nhtoc.com/vbforum/search.php?searchid=94117
I found the following on another site though:
Ford Harley-Davison Trucks - 2000-2012 F150 F250 F350
2000 --- 8197
2001 --- 6381
2002 --- 12,505 (Black - 6253, DSG - 6252)
2003 --- 10,047 (Black - 5024, Two-Tone - 5023)
No real info on 2002 & 2003 of how many for each color option. Ford usually does a 50/50 split unless it specifically announces a limited edition color option, in which they say how many will be made. Then with the 50/50 split if total production is an odd number then the Black will be higher then other color option done.
So as for rarity --- 03 Two-Tone is the rarest with only 5023 made.