Starting a whole war just to kill Viper would seem a bit excessive if you ask me.

The war is just something to use against him that's why they want him dead the war is a part of the plan to kill viper

Why do they want him dead then? What is the enemy faction's motivation to take out the protagonist? How about their long-term goals. Why would a genetics company be linked to this Viper character?

I believe your idea has merit, but you have to explain away these questions in some manner that can be accepted as truth. MGS is a very convoluted series, but it does make sense from a psychological and motivational standpoint.

The fact is viper is a foxhound solider chronotech wants foxhound dead and viper is a foxhound agent now viper is the son of an incredible american soldier

...Why Chronotech and not XOF, the task-force that seceded from FoxHound and sought to eliminate all major members?

I'd like to make a new corporation for the metal gear series

But why the name Chronotech? Do they make expensive watches as a cover-story or something? Or are they invested in Time Travel?

They make superwarriors