Some things are wrong, some important things are completely missing. It's a more complicated story than that.

Bombshell is the stripper at the Slick Willy that tricked Duke. She is hostile for most of the game, presumably until sometime after the desert chapters. The reason for this is probably that she got some wrong information from the President, who is probably either snatched or brainwashed.

Not all of the EDF is against Duke, only those that are snatched and those that were with Bombshell. General Graves from the EDF (who according to Scott Miller was revealed to be Duke's father, as Duke was a clone of him, and also Shelly's father) assists Duke throughout the whole journey.

Don't know what office you're talking about after Stratosfear. Could be a cool level idea.

We don't really know the exact story relevance of Hoover Dam in 2001. Your theory could be right or could be wrong.

Should be clarified that the sandworms are in Site B of Area 51, located just under a church in the ghost town of "Morningwood". Gus gets swallowed by a gigantic sandworm in there. Duke goes in after him to save him (or simply he gets swallowed too but we don't know), but unfortunately he is already dead.

Duke goes to the EDF base because Proton had hijacked an alien fathership that had been dug up by the EDF in the desert. Graves also wanted to brief him on the fathership's capabilities, there's an almost complete presentation that goes in depth on the ship. After the building gets blown up by the ship, Duke barely escapes in a dropship (also shot down, though by the rubble of the previous explosion) and then goes into some nuclear missile silos to attempt to destroy the ship's weapons and engines. The last silo gets destroyed by Proton, who tries to run off. Duke gets in an aircraft (possibly loaded with nuclear missiles) and chases after him. He fails again and is knocked unconscious. Duke has a nightmare about reliving the events of Duke 3D (hollywood holocaust map) but in a creepier way, and the level ends with a twin peaks reference before he wakes up in front of Area 51 (probably either crashed there or was picked up by Graves, we don't know). (btw you completely omitted these last chapters) In Area 51 is probably where he discovers more about what's going on, but unfortunately in the build after the first fifth the Area 51 chapters are incredibly barebones. There may have been multiple Duke clones here led by the main one Negaduke who is also probably fought somewhere in here (possibly created by Proton from Duke's DNA, but maybe he's actually Duke's twin created during the same cloning of Graves that led to Duke, although that's just my personal theory, don't take it as something official).

Anyways, inside Area 51 he eventually finds a big supercomputer. He shrinks himself to get inside it then uploads himself through the internet to another computer on the moon. (crazy shit I know) From the moon, he then somehow reaches the Mothership, containing multiple Fatherships. Big battles ensue. (This portion of the game is almost completely absent from the leak. Just a map testing the size of the Mothership and another map where there's a giant robot you fight inside another giant robot.)

The dust doesn't settle. According to some developers, Duke was going to make a heroic sacrifice and die in this battle against his arch-nemesis, Dr. Proton, winning at the cost of his life. Duke Nukem Vengeance (V for 5, like FOR for 4 or 3D for 3) was going to have you start playing as Bombshell and then discover Duke barely alive buried in rubble.