I'm making the following assumptions.
While there is a lot of guesswork that can be made, what you have put down in your post is pretty steep and rather contradictory to canon.
Well I expected it to be controversial but contradictory to cannon I'm not sure how.
Ancients:
Not from this galaxy
I have not come across anything that suggests they were not from this galaxy.
Have you come across anything that say they were from this galaxy? If they could explore a decent part of their galaxy before discovering subspace it's logical that they may be from a smaller galaxy.
Explored most of their galaxies usable systems and moved out into neighboring galaxies.
This appears to be true according to 
Well we agree on this at least.
Shivans:
Creatures that live in subspace
No evidence save speculation, even in canon sources.
No but no evidence against it either. Maybe they weren't native to subspace but evolved to live there. Maybe they were created to exist there or enforce some other species laws.
Do not require node or anything else to travel to and from subspace
No, however they are able to use nodes that Terran and Vasudan subspace drives cannot, at least as far as canon has stated.
Only use the subspace nodes to track and follow us.
Nothing to support this. They do have subspace tracking, but they use the nodes same as we do.
Again nothing to disallow the theory. Command in FS1 wondered how they bypassed some of the blockades. Not needing our nodes could be a reason.
Attack any race that disturbers their domain
No solid info available to support this. Their motives have not been fathomed, and they cannot unless they open communication. So far, appart from Bosch's ETAK project, they'd rather fight than speak.
Yea but I'm trying to fathom. Maybe the took Bosch to extract intel about our subspace knowledge from him.
Vasudans:
Slave race of the Ancients brought to Vasuda Prime from their original home world.
Speculation, cannot and has not been confirmed, save that they may have had contact with the Ancients in the past.
Only a theory. Seemed to be a good one and opens up campaign ideas.
Terrans:
Native to Earth but experimented on by the Ancients.
Experimented on us to what end? There's nothing to suggest they even knew our species existed.
Well I have a couple of theories on this. First is they tried to eliminate us by biological warfare. It wiped out the neanderthals and caused the bottleneck we see in the evolutionary timeline. Maybe they say the neanderthats as more of a threat then then us. Second we were close to their species and they were doing genetic experiments on us to speed up our development. Maybe they need troops. Maybe we are just a petrie dish that didn't get sterilized.
Knossos:
Device created by the Ancients to create subspace nodes.
We don't know if it was to create nodes for sure, or merely to stabilize existing ones. The info has not really been clearly explained for sure.
No we don't but one thing the game shows is that the jump nodes with Knossos devices seem to only lead to one system. Systems without them seem to have many more destinations then nodes. It's not on the maps but in the briefings. One system is said to have more than a dozen destinations from its node(s)
I'm afraid that kind of shoots your theory full of holes, but for the sake of argument:
It may show some doubt but those shots weren't lethal.
Theory:
Ancients created Knossos devices to open subspace to them.
I think you should say more like give them increased access to subspace.
I was thinking more along the lines of they discovered the existence of subspace then experimented to find a way to travel from system to system faster. That is where the Knossos comes it.
They left their own galaxy and made it to ours.
Again there is nothing that positively states they did not origionate in our galaxy.
No but there is nothing that says they did.
After exploring part of out galaxy and several others they invoked the wrath of the Shivans for disturbing their native environment.
There is nothing definitvely placing subspace as the true home of the Shivans. The Shivans may be merely advanced xenophobes that just happen to be sensitive to subspace.
See above
Final battles were fought across the galaxies.
All we really have for sure is that after the origional battles, the Ancients retreated, eventually abandoning their empire.
Yep and an empire that expands galaxies cannot be abandoned all at onces. Surely the battles were fought on multiple fronts.
In a last ditch effort the Ancients tried destroying the Knossos devices to stop the Shivans. This is why there are no Knossos devices in the nearby systems.
Why not just turn the things off? As well, why build a Knossos if there was no need, which they may have felt to be the case?
Maybe it has to be turned off from both sides. Maybe they were needed but no one ever thought the nodes would stabilize and the Knossos would no longer be needed. Maybe the Shivans not knowing what was going on stabilized the nodes from within subspace.
Unknown to the Ancients the Knossos devices once turned on for a period of time stabilize the node and are no longer needed.
If they created the technology, isn't it likely they would have a very good idea how it would perform?
Well when we made the first Nuke it was theorized that it could ignite the entire atmosphere. We still did it and still don't know all there is to know about nuclear energy. It's the we built it, it works, leave it alone philosophy.
The Knossos the GTVA discovered was one of the last built and never turned on.
We have no way to prove this at all.
Yep.
The Lucifer fleet was a scouting mission to see what was causing new subspace disturbances.
I disagree - the Lucifer and its fleet was way too big for a scouting party. A scout would quietly drop in, snoop a bit then bug out back to mommy, not commit major resources to an extermination campaign.
I can't believe I'm going to say this but I have to agree with Trashman. Even if it wasn't stated what is a scouting party? A small force sent to check things out. If you have 10,000 ships it could be 100 ships. If you have 100,000,000,000,000 ships...
When the Sol node collapsed it sent shock waves through subspace.
Possible, however subspace and how it works is still up for debate.
I'll post about my theory on this later.
Maybe these waves hurt the Shivans just like dropping a stick of dynamite in a pond of fish.
Not enough information on the Shivans to predict with accuracy. It could just as easily have no effect at all on them.
Again yep. It's just a theory and relies on the Shivans living in subspace.
Between FS1 and FS2 the Shivans assembled. They would have come no matter what but when we created a new subspace portal the Sathanas fleet closest by was angered and attacked prematurely. When the rest of the fleet arrived they saw us try to destroy a subspace node. Fearing that we would succeed they came up with a way to counteract the subspace shockwave by destroying the star. Their ships being capable of feeding off of a stars energy formed a ring and drew enough energy off of the star to make it collapse. The resulting collapse resulted in the supernova. Shivans go back into subspace to lick their wounds and build and gather an even stronger fleet.
Anyone's guess, but it just doesn't work for me. I still favour the supernode theory. The Shivans weren't so much sucking energy away from the star, more creating a subspace field around it. I'm not really sure that the Shivans were so much in terror of destructing nodes either. You would tend to think a supernova would likely destroy any nodes left in the viscinity... As for licking their wounds and building a stronger fleet? 80 great bloody juggernuts plus escorting fleet units and screen is a pretty darn powerful fleet don't you think? The GTVA certainly never mounted much in the line of successful challengers.
I alway like the supernode theory as well. It still may be the best one but the beer was telling me otherwise
As for your ending questions:
