Tested your gems a bit and here is my opinion :
Chaos emeralds are fine the way they are, except that you can't make the master emerald once you make one chaos emerald separated.
Your blocks and items are using IDS that are very close to vanilla, which is not good. Switch to Forge 4096 block IDs fix and make items IDs at 10000 range.
I couldn't find the "mystical generator" to extract energy from mystic gems. Mystic gems are useless at the moment.
I've said this before but here it is again, remove gems ability to store energy. It is pointless as there are many other cheaper ways to store energy and gems with energy storage makes them (usually) unstackable which is bad.
On later versions you could mess up with stronghold/end generation code and try to make raw chaos emeralds generate there instead of using the egg as there are ways to duplicate the egg. Also by permanently using the egg it removes the utility of a GT generator (dragon egg siphon).
Master emerald should be the one that is obtained by defeating the enderdragon (aka when dragon is defeated it generates the altar AND a raw Master emerald beside it).
decided against the mystical generator remember, just slot em in where you would put a battery. I also realise there are cheaper ways of storing energy, just thought that this is a cooler way of storing energy, besides for those who are running trading mods, its much more fun to trade gems that store power than batteries... i will however re-look at creating a mystic generator if other people think it will be a better way of doing it, i just dont have much free time at the moment as i have a baby due in a few weeks and a new job starting a week monday.
I also realise that the egg is used by GT but not everyone uses GT and those who do will simply have to make a choice. same with the master emerald. i dont want people having a master emerald AND chaos emeralds... be super OP. you can make the choice... a master emerald or 7 chaos emeralds... i am also not responsible for glitches in duplicating the egg, it is cheating and so i am not going to change the key ingredient.
i will definitely look at end/fortress generation though and like i said, will take another look at making a mystical generator. you have had lots of great input SpwnX, thank you it has really helped having someone who is honest and fair with their evaluation