Lets start chronologically with ENT Shockwave.
It is a strange timeline.
As it contains several premises:
1. no advanced computer technology -> Humans disappear in the 22nd/23rd century
2. knowledge of the Romulan Star Empire
3. buildings are mostly the same -> millennium old buildings?
There is the problem with the Xindi. By this point there are already set on sending a probe.
It could be explained that the Sphere Builders persuade the Xindi to use the bioweapon. It would take perhaps several decades and by that time Earth has the opportunity to learn of the Romulans.
As it is we have a similar development of the Vulacan Protectorate seen in Forgotten History.
V'Ger shows up does not find anything on Earth, so it continues its search for the creator...
Delphic Expanse covers the entire galaxy.
In thousands of years the shockwave created by the Body Electric destroys all life.
As to what happens to the Borg, Caeliar, Q,... your guess is as good as mine.