In the final main mission
I opted to kill Michael, and now he seems to be dead for good.
Is there anyway I can still play the Epsilon Program stranger missions or do I have to start all over with a new game?
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If you still have a savegame from before you made the final choice, you can load that save to play the Epsilon missions without starting a new game.
If you no longer have such a save, i.e. you overwrote your only savegame with the endgame save, then you unfortunately have no other choice but to start a fresh new game.