Yes, GrandMA2 is definitely that way, that you have to use 3 digit cue numbers even if you are not using anything but the first digit.
I am also thinking using MSC is going to be painful. Trying to understand what happened. You have a show that has 1000 presets already built in catalyst and you just need to trigger them from the ma in order? Or do they jump around and go out of order all the time? Do you need the console for anything then? couldn't you just use the mouse and trigger everything in cat? Or is there very specific timing?
If it is all timed out already in cat and all you need to do is trigger to timecode, maybe use something like Qlab and send a MTC timecode...