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.
Ancients:
Not from this galaxy
I have not come across anything that suggests they were not from this galaxy.
Explored most of their galaxies usable systems and moved out into neighboring galaxies.
This appears to be true according to
Shivans:
Creatures that live in subspace
No evidence save speculation, even in canon sources.
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.
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.
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.
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.
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.
I'm afraid that kind of shoots your theory full of holes, but for the sake of argument:
Theory:
Ancients created Knossos devices to open subspace to them.
I think you should say more like give them increased access to subspace.
They left their own galaxy and made it to ours.
Again there is nothing that positively states they did not origionate in our galaxy.
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.
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.
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?
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?
The Knossos the GTVA discovered was one of the last built and never turned on.
We have no way to prove this at all.
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.
When the Sol node collapsed it sent shock waves through subspace.
Possible, however subspace and how it works is still up for debate.
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.
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.
As for your ending questions:
Will we figure out how to destroy the Shivans in subspace?
Um, find em and shoot em?
Will the Shivans figure out a way to prevent the destruction of the nodes?
Don't let them get blown up?
Will the Vasudans find the truth about their true homeworld? Does it still exist?
I have doubts that this is the correct supposition, as the Vasudans are quite well suited for Vasuda Prime's environment.
Are there other surviving races just around the corner? Are they friendly? Are they more advanced but smart enough not to use subspace?
Who knows? Friendly or not, this depends on if any are found at all or even exist. How do we know that subspace use is stupid? Perhaps the Shivans just hate everybody whether they can use subspace or not.
Do the Shivans have masters or allies?
There is no info regarding this at all. Masters of some kind, anything is possible. Allies? Maybe they have found another race they didn't shoot on sight...
Are there any Ancients left? Could a few have survived on far off isolated worlds that don't have subspace nodes?
We do not know, but if their empire was a enormous as the cutscenes claimed, then it is not terribly unlikely that there were some surviving colonies somewhere.
Just some things to think about and argue over for the new year.
There - officially deliberated about and argued!