Well, I've reapplied the thermal paste and reseated the HSF a few times and while I have gotten the overall temperatures to drop, I still get the same strange temperature spread.
Here are the new temps
Idle Temps (stock HSF - AS5)
Core #0: ~39C to 40C
Core #1: ~32C to 33C
Core #2: ~39C to 40C
Core #3: ~32C to 33C
As you can see I'm getting much better idles temps than I was before. I used the line method for applying the thermal paste. With 4 attempts, 2 using the line method and 2 using the center blob, the line method seems to produce lower temps for me.
Under load running Prime95 none of the cores went above 75C, but the same temperature differences between cores remained with one core sitting at around 68C while under load. I'm happy with these new temps overall, but I wish I could get all four cores to match the lowest temps. I've considered 'lapping', but have never done that before so I'll just be content with what I've got.
I have read on a few other forums that I'm not alone and other people (a few) seem to be getting odd temperature spreads with the new i7's, so at least I'm not alone.