Since the DVD doesn't have the Krypton sequence, you can go straight from the credits to the following edit:
Chop Luthor's Vanderworth Extortion sequence. Totally unneccessary. We don't need to know how he got his money, just like we don't need to see how he scored Kitty or how he gathered the group of thugs he has. He's Luthor. We'll roll with it. He's currently, SUCCESSFULLY plotting to create a new continent in the middle of the ocean while breaching the Fortress of Solitude. We'll be fine just assuming he swindled someone for cash or flat out robbed it.
Plus, this edit is REALLY easy because the ringing note at the end of the opening credits is the SAME as the ringing note at the end of the Vanderworth sequence.
So this means we go straight to Ma Kent at home. maybe reinstate some of the scrabble footage between the establishing shot of the homestead, but before Ben Hubbard drives off. From there we stay the same.
Reinstate some of the original intro to Luthor and Kitty from the Deleted scenes, and then cut to the "Fire from the Gods" conversation as it is in the film. This way you establish the dynamic between the two, and it serves as a better intro AND gets the villain plot rolling a lot quicker.
When Clark wakes up and looks outside, cut the flashback sequence to young clark learning his powers. Useless and unneccessary. Also cut Superman throwing the ball too far for his dog to catch. That's just Superman being a dick. Yeah, it's knee-jerk funny, but why would superman do that to his dog? Instead, reinstate the deleted scenes that show him wistfully staring at the ship, and then walking into the barn and reading the papers.
Cut from there straight into he and Martha talking, and then cut in the deleted scenes of Ben interrupting with his flowers, and Martha telling him a) She's moving to Montana and b) he's put there for a reason--use the much better dissolve to Metropolis. This cut highlights all of Clark's reluctance to even BE SUPERMAN. it heightens the drama because Clark isn't simply just trying to get Lois back all movie--he's trying to prove to HIMSELF as well as everyone else that the world DOES NEED a Superman. Even if he's reluctant. The self doubt doesn't take away from the romance angle, it enhances it, as well as enhancing the rooftop interview, the initial re-introduction to the Daily Planet, and the emotional payoff of the Plane Sequence. Now it's not just that he's saved people and returned, it's that he's saved people, returned, and proved to himself he's needed--that THIS is what he should be. That his mom was right to kick his ass and make him go to Metropolis. This also changes his reaction to finding Lois' desk: instead he's not pissed about the article--he's freaked about the kid surprise. It's not the ARTICLE that makes him run to the bar--it's the KID and HUSBAND that throws him.
When in Metropolis--take the time to re-insert the shot of Clark looking at his superman suit while in the closet. You might have to snake this from the trailer, since it's not a deleted scene.
After Clark hits metropolis the only real big cut that I think people would dig is the "Stalkerman" sequence where he's listening in. Honestly, you don't really need it. Tricky sound editors can use existing score to segue from him flying down the street of Metropolis, past the Daily Planet, and then cut up into the sky to his trip to the listening post. You can even pull some of the Brando voiceover out and replace with different music to change the point of the scene from him feeling shitty about Lois rejecting him, to him feeling steely and determined about returning to his job as Superman. Moving the bank rescue closer to the plane rescue also gives you more of an idea that Superman is BACK back.
I'm sure there's other little trims here and there, I can't think of any of em off the top of my head. The next big string of edits is this:
You cut the hospital sequence, instead going from Superman's body, prone in the crater, fade to black, and then hard cut to "Superman is Dead" and the scene plays out as normal until Richard approaches Lois, and Jason gives Lois the drawing. CHOP OUT ANY TV FOOTAGE. Keep the audio, keep Lois looking up at what we know is the TV offscreen, but do not show the TV footage. Cut to Richard saying "You don't have to be here" and then cut immediately to Lois looking at Jason's drawing, as it pans down the chain of cartoon people. Once it gets to Jason's self portrait, cut IMMEDIATELY to the 3 of them in the car driving to the hospital. The scene plays out as it normally does from that point on, ends up increasing the emotional content of the sequence because going straight from Superman's Body to "Superman is Dead" is a pretty fierce little cut there, and then revealing the size of the crowd as Lois walks into it and the camera cranes back to really show us the expanse is a much more powerful reveal of that crowd then by seeing it on a flatscreen at the Daily Planet first.
Cut out Lex and Kitty on the island. No one cares anymore by that point, and the closure is garbage, beacuse it's essentially a 2 minute dog-eating joke and that's it. It's enough that he got away. We know he's also gonna get away from the island, too, so the end point ends up being exactly the same as if the scene never existed.
So as Jason and Lois leave the room and the door shuts, immediately cut to the nurse walking through the halls to Superman's room, and let the end of the movie play out as it does in the film from that point on.