I think the picture quality of the projection was better this time around, although I noticed a faint horizontal red bar that kept sweeping from the bottom of the screen to the top. It wasn't too distracting but I did notice it throughout the night.
The re-cut episode was great and really flowed well. Going straight to the deflector dish firing after Riker says "fire" was the right call. The lighting was a bit darker than I remember in some spots but it definitely added some nice atmosphere.
As for the upscaled three seconds, it seemed a lot more noticeable to me than the 13 seconds which were missing from Sins of the Father. Still, it was only three seconds so it's not really a big deal.
All in all I had a great time. Can't wait for the next screening in July!