Well the only thing left is the gear change. Your RPM's are way lower at part throttle than they were, leaving you down off the converter while cruising. Either way, I think you would be experiencing this even NA.
I know when I went the other way, from 2.76 to 3.55, the difference is quite a bit in RPM's at 55-60 mph.
Now that I think about it, perhaps it was lower compression for boost.