Until Cloud's appearance, the Raven was broken and could not be found.
When Cloud arrived and the Raven activated (as you saw in game), it became able to be found.
Your decision to go on a ship was wise, because with magic in its state it is near impossible to locate and teleport to someone moving at sea. Flying around to find them at sea also difficult since you can't have a lot of spells active at the same time.
So until you came to port, Malchia (or whoever) would not have been able to easily get to the Raven.
GOLK wasn't looking for the Raven, rather looking for Cloud. Why he waited to attack until he did, since he can obviously find you has a few answers revolving around the time and your location.
Note there are always a lot of different ways it can go. As I noted to Zunder, had you ever let Gnelson tinker with it, things would have happened.
Who you sent also mattered. Sending different people would have had different results.
Where you went mattered. Had you stayed in Ermaneo, gone over land, or sailed to Pacyr, any number of different things would have happened.
Who went back to change things back has an effect on what if anything reverted back to standard.