A, not so, simple solution would be to do the following.
1: let your world generate as normal and play on it for a while to generate land around you.
2: when your ready to explore Mystcraft, go into the config files and turn "OFF" custom ore generation in the COFHCore config file.
3: create a mystcraft age to explore with the custom ore gen off
4: turn the custom ore gen back on when your done exploring that age.
While the custom ore gen is turned off, and handled by vanilla minecraft, the mystcraft ages will have a much higher chance of being stable. Meaning you should be able to actually get stable random ages. This is not a full solution though... When the custom ore gen is turned back on, the ages you already have will most likely gain instability as well. And it requires that you shut down and restart the game every time... If only there was a way to whitelist the custom ore generation for only the overworld, end, nether, and possibly the "promised land" and twilight forest. That would make it a lot easier.
Edit: Ok, that was dumb of me, slightly simpler fix. alter all the ore generation json files to white list them. In each spot where it says dimension restriction: blacklist, change the blacklist too say whitelist instead. then just change the dimensions from what it currently says, 1 and -1, to say 0 and 7(twilight forest). Once this is done, mystcraft ages will no longer generate using the custom ore generation and should not suffer from the same instability problems. Note: this is not a final solution, but should be a workable stopgap allowing Mystcraft exploration again.