Regarding the DNA part. David was a survivor of the original philadelphia experiment. His DNA was needed by Mailer not to simply travel through time, but so he could SURVIVE the trip to the past as well.
-- "So Mailer sends a Stealth fighter back to the Germans in WWII so they can win the war, creating an alternate timeline"
This is the misconception many have about the movie. In the original timeline, Mailer is working to perfect Longstreet's experiment to make an object disappear and reappear somewhere else. He shows the military officers how the soviets built a system to detect stealth bombers, and how his machine can instantly deploy aircraft anywhere in the world. The military still wants to cut funding, so Mailer sets it up to make a nearby stealth disappear and reappear over rammstein air force base in germany so they take him seriously. -- As it turns out, while the plane was teleported over germany, it was also sent back to the same day/year the philadelphia experiment happened in 1943. Ironically Mailer's father is the one that discovers it.
-- "But it's still a timeline where Mailer is unhappy enough with the timeline that he wants to go back and alter it again. Good thing for Herdeg that Mailer didn't get it right the first time or he wouldn't have built a time machine at all in the alternate timeline."
I can't recall the exact conversation, but when David meets Longstreet in 1993, Longstreet explains the events after David disappeared in 1943. 24 hours after David's ship disappeared, D.C. was nuked by a plane called the "Phoenix" that Mailer's father found in Germany, and claimed he built himself. His father didn't know how powerful the bombs it carried were, and the stealth was caught in the blast when it bombed D.C. He was a hero at first, but was ridiculed and disgraced when he couldn't build another stealth or a nuke. Some time after his son was born (Mailer) he committed suicide. Longstreet said it took him 20 years to figure out the Phoenix was a future aircraft that was pulled back as a result of the experiment.
Because of his father's suicide, Mailer studied the philadelphia experiment so he could go back to 1943 and inform his father so that the stealth keeps a safe-distance and survives, and his father keeps his honor. Mailer never seems aware of the original timeline where america won the war, or that his original self was responsible for the stealth accidentally getting sent back in the first place. Longstreet didn't know either until David told him.
-- "Another question is why didn't the Germans capture Herdeg in the alternate timeline when he first jumped from 1943 to a German-controlled America in 1984? Alternate Longstreet still knew about the Philadelphia Experiment so it must have happened in that timeline."
The Philadelphia Experiment happened in 1943, exactly one day before D.C. was bombed and the timeline altered. Mailer and Longstreet never knew there was an original timeline. When David meets Longstreet in alternate 1993, Longstreet thinks David has reappeared that same day. He and Mailer (somehow) knew that David would reappear in santa paula on a May 4th, but didnt know which one, so to them it was like he was sent forward 50 years instead of 40, and reappeared in that house. David later explains to Longstreet that an original timeline existed where America won the war.
This is the best I can explain it, but if you see it again pay attention to the conversation David and Longstreet have when they meet in 1993. That bit of dialogue is what clears up the movie.
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