The SE version has a more overall openness and air to it. The wire used in the Amphora is a 22awg OCC solid core copper in a PVC jacket, the SE is a 22awg solid silver that is pushed through a cotton tube. Its exact same stuff I use to make (made) my ALO Cotton Docks and Cotton mini to minis with. There are a few members who have the SE but I do not think we have had any direct comparisons via the public yet.
Hope this helps.
Forgive me having to go from memory (never a good thing) on the non-SE, but I agree with Ken's feeling that the SE has a bit more air. The "ah-ha" moment for me came when listening to a well-recorded classical guitar cd. I got a bit more finger-plucking-string and fingers-sliding-over-frets feel with the SE...not in any kind of spotlit or hyper-detail sense. It contributed to the overall ease of the presentation and aided in the act of suspending disbelief. This is WELL up the diminishing returns curve, but audible. I loved my dad's Amphora so much it was an easy decision for me to talk to Ken about the SE.
I've been made fun of earlier in this thread for commenting on how beautiful the amp is but I could care less - this is a beautiful piece of audio art. My SE case started out as a solid piece of claro walnut and I think the end result is stunning. Many thanks to Ken and Vinnie for a life-enriching product.