OK, I finally decided to give the new version a try, and dear sir, It's a monster.
The repositioning of the SAG and switching from Kirov to Kiev changes everything. And the first three hours where nothing but enduring missile strikes, avoiding enemy subs just under my ships (did you tweak their teleport zones or was just bad luck on my part?) and making hastly planned and in the end uneffective ASuW strikes.
I lost all the STANAVFORLANT and all the Invincible escorts. The carrier itself along with the last SAG survived and that decided me to continue. During the following lull I lost two subs to the Soviet SAG (again) and attrited it to death with Harpoon and Sea Eagle missiles (also again), Forgers are able to deny airspace to enablers and patrolling MPAs (as opposed to striking ones) but no more than that.
Once the SAG was sunk things more or less switched back to routine except that it's last ditch missile attack literally depleted my ships of SAM (last few missiles were confronted only with chaff and CIWS). So I had nothing to defend me from the next bomber raid except less than two dozen fighters. Half of them armed only with Sidewinders.
I did it [8D].
I managed to position and sustain a CAP north of parallel 70º, with Tornados coming all the way from Scotland. The rest of the fighters from Bodo and a Flanking Invincible, and I strangled the strike in its craddle

.
After that, it was a waiting game for the amphibs arrival and unloading, with a moment of sheer terror then some Soviet strike fighters decided that the ships were much more valuable targets than the rubble of Andoya and the other northern bases (damn ruskies with a working brain).
Triumph at the end but a damn bloody one.
Now relevant points:
Great idea the changes in position and composition of the SAG, it covers both the bombers and the submarines.
The munitions cut in Bodo it's very annoying (as it should) but it's still posible operate all Phantoms and Eagles from there during almost all the scenario duration. Not having Tornado F.3 munitions there, was a nasty surprise (as it should).
The problem of kamikaze MPAs is solved. Only once I saw one, overflying Norwegian bases (and the fool even survived since it did it when there was no ready interceptors [:D]), so you can chalk it to a fluke and call it done.
I put a Side level doctrine forbidding refuel and UNREP to avoid whatever happened last time, until the devs give it an eye. The ships have more than enough fuel to make the trip at flank speed, so you should delete or put back in their groups the tankers. Micromanaging them it's very annoying.
As of right now the biggest problem is, and sorry for the bluntness, one of boredom. After the frantic start you have more than a day to recompose yourseld, destroy the SAG and preparing for the second round, and that it's a little too much. Not sure what can be done without excessively beefing the enemy.
But the worst offender it's not that but the time after the second strike, when you still have more than two day of play and probably more than one for the amphibs to arrive and unload. I played all that time on the background while I was studying Chemistry [:-].
Here I do have a pair of suggestions.
First, cut in half unloading time. Not realistic, I know, but this one seems to me one of those times when you have to compromise for sake of enjoying the game. You can (and should) cut a day from game time to maintain the time presure. Also put a special message indicating the completion of unloading and perhaps another informing of the start when the ships arrive to the landing zone. I play with events not visible and I only discovered that the ships where scoring when I happened to check the scoring log.
Second, once there are ships in the landing zone, reassign all tactical strikers to anti-ship duties. Some Fencers did it accidentally in my playtest and they managed to damage several escorts.
Third, SSGNs shouldn't play to be SSNs after they expend their missiles, I'm not sure if there whould be enough time to do it but you should try rearming them. Give them a home base in Kola with proper magazines, and a retreat doctrine to send them to base when their primary offensive weapon is depleted (and lets hope the devs have programed them to consider only their missiles as primary weapons).
All this would make the second part of the scenario much more engaging. Also much more deadly, so perhaps you should put some extra ships with a readying time of twenty hours in Scotland and use them as reinforcements.
All said still a good scenario as is, is just the lull on the second half annoyed me to no end.
Hope any of this helps you, and again thanks for your work.
Ancalagon