umm no, thats not how it works. It does not matter if the base weapon damage is black, or any of the elemental types arcane fire holy poison cold etc. You do not gain more damage based upon what type it rolls, only how high or low and if there are any additional rolls such as IAS, dmg% that will effect the total weapons DPS. This weapon having 1385-1728 holy damage INSTEAD of fire would NOT benefit you in any way despite having +Holy dmg gear on. I truly hope you didnt sacrifice some better weapon for a holy dmg weapon that sucks thinking your doing like 4x the normal dps because of this.
Anyway grats on the flail, I made a shotgun sader few weeks back somehow got lucky enough to have all his gear drop in 2 days of chest runs with a 2800 flail. He does pretty nice, but I put him aside since my other chars like WD/DH are more enjoyable to play for now. I had a shotgun sader have the perfect hellskull shield drop today though. 10% CC 8% CDR 15% HF dmg 740str with +wrath secondary.