The justification given in the show for the whole mess with the jumps was that every few hours, the Galactica would send an update to the rest of the fleet to compensate for stellar drift. So the plan was to go back, compare the star charts, and extrapolate the fleet's position from that.
Going by that, I'm guessing that the FTL must need hyperaccurate data about the position of large gravitational forces, or they didn't have enough power to successfully compute where everything would be precisely enough to make the jump.
As for the network thing, the only justification I can think of is that in 'networked' mode, the computers accept/maintain connections, whereas otherwise they'd be completely closed, and that vulnerability was just enough to give the Cylons a certain amount of access to them. Considering the Cylons are sentient computers, it's not a bad guess that they're inasanely brilliant computer hackers.
But overall, I'm gonna have to go with "plot device" and "consultants were out to lunch" on this one as well.

Really, it's about as plausible as squeezing icky tubes to conduct interplanetary travel in a spacecraft meant to house only a brain.