OK, I've played through the Replicator missions. That is a lot of stuff to destroy. Especially all of those systems in a row. I don't think it's balanced at all. You might want to break these missions up somehow instead of having them all in a row. Maybe insert the first Atlantis mission in the middle? It's an excuse to go back to Earth for a bit.
And then award the cruiser when the player gets back from the Atlantis mission? The more powerful ship would also help with those very challenging missions.
And since the "Replicator systems" are given the Asgard color, I take it that means these were conquered recently by the Replicators? So why are they called "Replicator systems"? Shouldn't they have regular names like the other Asgard systems?
The powerful Asgard ships that are supposed to help tend to go into a corner and keep patrolling that corner. Sometimes you can lure a Replicator ship into the corner where they will attack it. But usually they just sail back & forth doing nothing useful. Maybe Campeador's suggestions could help you improve their patrol behavior.
Failing that, I think many more of those deployable SGC ships would be a good thing to make those missions manageable. I resorted to setting myself invulnerable and ramming the planets just to get things over with.
I had noticed the mission text getting cut off, too, but was more concerned with game mechanics on a first play through. I'll try to go over the jobs file and give you a complete list of typos and possible sentence improvements.
BTW, I've been told to deploy "Tealc's special fighter" a few times but I've never had one in my cargo. How is that supposed to appear?