I like points 1 and 2, but I have some problems with the other points.

Decker vs. Kirk - how do you want to explain that Decker simply accepts Kirk as a new captain, and in the end he lets him the Enterprise without problems and "commits suicide" ?

The SF tram station is one of my favorite scenes, so I'm not very happy that you want to cut it. Do you also want to cut out the new Vulcan officer (I don't remember the name now) ?

If you don't have the transporter accident, how will you explain that they are using shuttles instead of transporter ?

I agree that Spock's arrival should be a surprise. Maybe you could cut his scene where he enters the Enterprise and let him suddenly appear on the bridge ? However I'm not sure about the flashback idea, I hate flashbacks but of course it's your edit :-)

The entering of the cloud - I think the director's cut has this scene perfectly balanced from both SE view and storytelling view.

Also a little tip - Spock's tear scene. On the Director's edition bonus DVD many people talk about the scene, where Spock cries. But I never knew what the hell are they talking about :-) I had to check it frame by frame and zoom the video to see the tear. Could you change it to a closeup of Nimoy's face ?