Actually. Consider this. The experiment to create the augments for colonists has side effects. The nanotech upgraded the colonists but thee side effect was that the upgrading didn't stop. What if the process actually kept going until all of the subjects cells were replaced with nanotech. You would in effect have the first exo!
If Clovis brae then realised what they had and got a warmind to re engineer the nanotech into Siva. The ultimate upgrade for its colonists. Turning them into living, adaptive machines. Complete with all memories and skills for colonising any planet. However the clear mental instability the upgrades caused would likely mean that Clovis did indeed also implement that personality change that one of the researchers wished they could do to patient E. This would have been in the form of the memory wipe. Each time an exo remembers what they were, that everyone they knew and loved is dead and the pain of being turned into a machine they would just have another mental breakdown. Necessitating another wipe.
I think the big Clovis brae secret isn't that exos are copies of people. I think they ARE those people!
Proto-Exo's were used by the Ishtar scientists to explore the citadel and work on the Vex gateways.
I really don't feel that this viral outbreak is all that related to the Exo's. Bray would have had multiple research happening concurrently. The viral outbreak may just be a method for bringing Efrideet back into the fold - as she left to join a group of Light users who wanted to do more than kill.
Also at least one of the subjects has died.
Cayde has memories and quite possibly still documentation from when he became an Exo - it likely happened on Europa. He states that some memories remain after the reboot happens.
Exo 2 also alludes to an Exo on a Jovian moon, where they are burning bodies. He/She pretty much states they are a weapon.