IT'S not THAT hard to understand...Mother elf= made from Zero's Original Body's Virus data to eleminate the Sigma Virus infecting Mavericks. Which means the Mother Elf is 100% compatible with Zero's original body, unlike other Reploids who tried to merge with it. Then the Mother Elf is corrupted by Weil and turns "evil". Yet, is STILL 100% Compatible with Zero's original body. So when Omega, Possessing Zero's Original Body, Merge with Dark Elf, he doesn't mutate, because He's 100% compatible with it. Oh and, he didn't turn crazier. There are NO evidence that the Dark Elf altered Omega's mind.
Problem is, we can't assume too much because the sourcebooks says very limited things on Elf Wars and the Sigma Virus' Origin( The origin of it's creation.)
As for Sigma Virus....it's not so hard to understand either:
Zero was created with the Virus within him, at this point, the Virus had no name. At some point in time, Zero awakens with his precise mission being unknown. He is found by Gamma team, wandering in a forbidden area. Zero wipes out Gamma Team and is, then, met by Sigma. Sigma battles with Zero and as the Battle Climax to an End, the Virus in Zero, which still bears no name, is tranferred to Sigma. Zero(I ASSUME) is still a carrier at that point and so is Sigma. Zero is repaired by Dr.Cain and, from now on, Zero shows no apparent sign of Irregularity and is watched over by Sigma. The virus continues to spread and causes more MAverick outbreaks, Zero and Sigma keep on fighting while spreading it at the same time. At some point, Sigma decides to rebel against humanity. At that point, the Virus STILL has no distinct name and is just called Maverick Virus. Then after X2 or X3( not sure), It is discovered that Sigma is spreading a virus which turns Reploids Maverick. FROM THAT POINT ON, the Virus is called Sigma Virus because nobody in the X Games ever knew( and for that fact will nener know) that the Virus originated from Zero. Before The Virus was discovered, Everyone thought The Maverick Phenomenon was caused by errors in their brain circuit. Then The Virus ,which Sigma caught from Zero, was discovered, but since nobody knew it originated from Zero and instead thought it originated from Sigma, they called it the Sigma Virus.
The fact that Zero is a carrier will be found out many many years later at the end of the Maverick wars.
At least, that's what I understand, things that I have just said might be untrue and based on personal opinions.