There's a lot of great feedback in this thread, thanks everyone. I managed to get in some changes in response to your thoughts, and they are as follows:
-Staff of Nat Gann: is now silver, gives Dex +4, and uses Dex to hit and Dex for damage.
-Hellstroke Greataxe: now has the Cold Iron mutation, which it previously lacked.
-Hellfire Crossbow: now has Flaming Burst. I can see how Flaming was too weak a choice when the Scorching Ray was really just a neat bonus.
-Timeblade: now gives a 3% doublestrike chance.
-Epic Hellstroke Greataxe: now has the Cold Iron mutation, which it previously lacked.
-Epic Staff of Nat Gann: is now silver, no longer gives Uncanny Dodges (until we fix the way it works, since right now it is taking away your dodges), uses Dex to hit and Dex for damage, and has a crit range of 19-20.
-Epic Timeblade: now gives a 6% doublestrike chance. It was also supposed to have Improved Slowburst before but the mutation it was given was the wrong one. It now has Improved Slowburst as it should.
-Shield of Reflecting: is +5 now, and has a min level of 10.
-Wand of Blasting: now gives Greater Potency IV.
-The items that grant the Abishai set bonus that had energy resistance now give 10 resist instead of 3.
-Battered Guardian Shield: now has min level of 10.
-Goggles of Time-Sensing: now have min level of 4.
I always appreciate comments on the loot- I take as much time as is possible to read them and make adjustments.

Oh, and about the third item in the Sora Kell set: it was indeed determined that the chest that should have been dropping it was not doing so, but it's since been fixed. It should be dropping now, and can be found in the Framework quest. There were two weapons that were also not dropping, and they should show up as well (one in Framework and one in Eyes of Stone).