I tried reading the entire thread, but 36 pages is a lot to go through.. I don't know if anyone brought up the Zero series in depth, seems people prefer Classic and X, no problem as Classic is also good, X, outside of the 1st game, I find it to be aquired taste.
Anyways, Zero in the Zero games is a completely different individual from the X games, just wanted to point that out inxase it hasn't been stated.
As per the radio drama, Wile stole the original body and either replaced the physical robot brain with one that contains the Omega personality or reprograms him to become Omega, I cannot remember the specifics of this.
But X had already backed up Zero's mind for study and basically defragment it's partitions to find a cure for the virus that originated from Zero.
Because they currently have a rampaging Zero body with no conscience or morality, X comissioned a duplicate of Zero's body, as close as they can get atleast, and installed the backup mind of Zero into the reploid body.
This is partially why he has amnesia in the games, the memories have been defragmented more than once, perhaps countless times in simulation, along with personality profiles, and this is before even booting him up for the elf wars.
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This part is more my headcanon than anything else, in Zero 4, the opening shows a blueprint of Zero's reploid body, it looks very similar to the Original Rockman's body.
My theory is that since it is X who had comissioned the body's creation, he may have taken his own blueprints as a basis, either thst or some of his own technology made it's aay into Zero's new body.