JES, if you have been following me recently than you would realize most of your information is outdated anyways. That was back when I was creating my own timeline. If you have been following most of my journals, then you would of seen recently I have been moving towards following the Prime canon better. I don't accept anything out of TV shows and movies as canon (and in the case of the Abrams films, Alt-Canon). Every once in a while I do like ideas people present in the novels, although how they got rid of the Borg was a terrible idea.
The Machina do not create the Doomsday Machine. The Doomsday Machine is still created by an unknown race for unknown purposes, although I believe it was used for mining or something of the sort and it had a pilot, and someone forgot to shut it off. The Za'du (previously known as the Jularni) tried to control the Doomsday Machina when it passed through their galaxy in hoping they you could use it to end the Machina threat, but it ultimately failed and where forced to use the Machina's Hyperacceleration gate to send it to another galaxy (since they didn't have a way to destroy it). Whether this is the same one Kirk encounters is hypothetical.
The Machina are not blood thirsty killers and they are not alive, mostly because they are machines. They don't no pain or fear, or joy like organic lifeforms do. They are not necessarily evil, but they do have a tendency to make other species go extinct. Most of them are like drones, following commands from a higher up, but each unit has their own basic AI that adapts and learns the longer that unit is functioning. The first Machina created, General Ra's is the leader and has been around for thousands of years. They were created in this other galaxy by a now extinct species, although most of the design actually came from an alien life-form from another galaxy.
As for the Renegade, she exists outside of Starfleet. The group she belongs to works for the Federation and was commissioned by them, but they have little to do with Starfleet, although they have similar uniforms, ships, and sometimes the occasional Starfleet officer working with them. They are like another branch of the military, similar to the USA.
At one point I had considered having the New-Orleans Renegade as part of the line, but since scrapped that idea for a less restrictive approach. And at the time the New Orleans one was around the R-D had been destroyed years prior, sabotaged by an unknown terrorist group on its maiden voyage. The R-E wouldn't launch until shortly after the events of First Contact.