Here's the info I garnered for you working solely with the 3rd Ed. DMG:
The cost of a +3 Dire Flail is 36,690gp. 690gp for the masterwork dire flail and 18,000 for the +3 bonus on each flail-head (DMG, p184, Table 8-10). The Rod of Flailing (DMG, p197) costs 40,000gp. Under "Adding New Abilities" (DMG, p246) it states that a creator can add new magical abilities to a magic item. There are some stipulations for certain worn items, but in the case of our Rod of Flailing they don't apply. So if we take the 40,000gp for the entire rod and remove the cost of the enchanted dire flail we have 3,310gp for the remaining worth(40,000 - 36,690 = 3,310). The designers seem to favor nice, round numbers to make things easy so you might want to round the additional rod abilities from 3,310gp up to 4,000gp. So here ya' go:
Rod of Flailing
Caster Level: 9th; Prerequisites: Craft Rod, Craft Magic Arms and Armor, bless; Market Price: 40,000gp
-----
690gp for the masterwork Dire Flail
18,000gp for +3 enhancement bonus on 1st flail-head
18,000gp for +3 enhancement bonus on 2nd flail-head
4,000gp for the weapon transmutation and "once per day defensive" abilities
This formula seems a bit crude to me (despite the fact that I just made it). It is both balanced and easily applicable to item creation, however. Let me know if this is what you were looking for and whether or not it was of any help.
===[Mr.Binx]===
"I think, therefore I think I am."