Wow you definitely have a better grasp on the technology than I do. I cobbled together the basic hybrid edit in just 4 days but that was just scaling up the SLV scenes using After Effects with no digital cleaning.
I left out Kirk’s, “Oh my God.” in the transporter accident because I didn’t want the SLV footage to sit awkwardly across the rest of the scene and I didn’t want to use the scaled up footage for the whole scene. I also left out the bit where Chekov talks to the crewman at his station before retaking his post as it sits awkwardly on the soundtrack of the DE. Fortunately McCoy’s line about them being ten miles tall fits in fine.
I think I managed to fit in most of the extra stuff from the ship. I haven’t touched the Klingons though.
It was easy to add the DE red alert claxon over the extra V’Ger attack footage alongside the red alert voice from the SLV. I managed to bleed some of Uhura’s dialogue either side of the DE footage too so it all runs along a fraction more rapidly.
I had to work a bit to equalise the hum of the ship in some of the SLV scenes but it was doable.
Mine is a real hatchet job. If you have been able to clear up the SLV footage, it should look great!