Well, if the story were to start from the FS2 universe I'd suggest somthing along the lines of this (although your idea is pretty good as well):
The Knossos portal under construction in Delta Serpentis, but this isn't where the problem arises. If we take a cue from the original theory that the Shivans were actually trying to protect subspace, and then project it to thefact that the GTVA is actually causing severe damage to it via subspace usage, then the most likely place for a tear to occur would be at the heaviest usage point. This would most likely be with Delta Serpentis and any other system, as civvy traffic would be greatest around there.
Now, remember in Trek exactly the same problem was occuring? The subspace tearing and what-not?
Now....the Knossos prepares to go online for the first time, bringing access to the Earth system via subspace.
At the same time, in a universe totally different, the Enterprise E is called to a medical emergency to a system some light-years from Earth. At the time, its near Earth, the lagrange point between the Moon and the earth to be precise. its docked in for some repairs. Captain Picard decides to engage full warp to the system, not wasting time. As the warp field initiates, it reaches accross subspace, damaging the already badly-hit fabric even more.
Then, somewhere else, the Rebellion fights the empire at Endor with a vast fleet of spaceships at there disposal. But they go up against the Death star. Little do they know the power source of the Death Star has direct links to a layer beyond normal space, something that is only known to a handfull of people....and the destroyers.
As the death star opens fire, the Enterprise engages warp and the B5 universe does , the Knossos portal finally comes online.
The GTVA sends a destroyer, the GTD Aquitaine through the portal to make contact with Earth on the other side. But it emerges into a very strange Earth, with vast blue seas and silver ships orbiting it; ships with saucers and pods to either side.
The Enterprise engages warp and slips through at several times the speed of light, but the flash that accompanies its departure into warp is odd, and the normal streaking stars during warp travel is absent, only to be replaced by what appears to be the rotating blue surroundings of a subspace tunnel. At the end of the tunnel, they emerge right back where they started: at Earth....but it is a far stranger Earth than the one they left it (read: B5)
When the Death star fires its first volley, it falls far short of any ship - instead vanishing in a bright blue flash and an open vortex.
Back in the GTVA, something strange is going on. The subspace Vortex generated by a ship as it passes through doesn't close at all. Instead, it remains constantly open.
then the Knossos device fails and self-destructs from the sheer energy pouring out. But the vortex continues to remain open. Slowly, the personnel gathered watch in horror as new Vortexes open up in front of them, and then remaining open. Out of each appears......Shivans.
But the Shivans are not interested in the terrans gathered, instead, they head from each portal towards the central one, first pouring in in pairs and singles, then ranging to the dozens, and then the hundreds. Every single class of Shivan craft - and some new ones - starts pouring through the new node. The GTVA then decides to send a probe through the node. It lasts just long enough to transmit an image of several more nodes inside the larger one, with Shivans heading through each.
It also sees a strange craft emerging from one of the nodes, an airplane looking much like a hammerhead, with a turret underneath the nose and another on its back. The plane is immediately followed by several black ships, all of which are trying to hit it. However, the black ships are stopped as the shivans engage them, pushing them back into the node they came from.
In each universe, Shivans appear, attacking everything and attempting to secure the area around the breaches. Of course, the universes fight back against the Shivans, but new breaches appear - allowing craft to move from each to the other. Now, in subspace, Borg craft appear to engage the Shivans. both craft being massively armed, and just generally massive, a fire-fight occurs, only to be interrupted as the SSD come through, opening fire on anything. Its immediately ripped to shreds by beams from a Vorlon vessel coming through another universe which in turn is hit by yet another ship from somewhere else.
Of course, our story is not here. Its with a pilot that are present in each universe (one per universe). Each is newly recruited to their respective forces, and each must find each other in the hell that has decended on their worlds, in order to bring things back to order - fighting the Shivans and even each other in the process!
But a larger secret lurks beneath the surface...one discovered by an old Admiral...one that was responsible for the suffering of millions. Nobody listened to him, but he was right....and now, the heroes might just end up destroying all the universes, instead of saving it!!
.............
Sounds lame, i know...but better than nothing.
