Looks interesting, and I'd be tempted to give it a try, but I'd probably need a demonstration of the rules in action. Maybe it's just my sleep-addled brain being slow but I couldn't comprehend them at all, let alone all the extra ones.
The basic rules are simple, and the additional rules are just refinements of the way the basic rules work.
Rule 1. Each crystal, you ask Gilgabot for a new job. Thus, after the 1st crystal, you have access to 1 job, and after the fourth and final crystal, you'll have access to 4 jobs.
Rule 2. Each time you get access to a new set of jobs, Gilgabot selects from that set. So, for the first crystal, it selects between monk, knight, thief, black mage, white mage, and blue mage. 2nd crystal is summoner, red mage, mystic knight, time mage, and berserker. 3rd crystal is Bard, ninja, ranger, geomancer, and beast master. If bard or ranger is choosen, you have to wait till you get access to them in a little bit to switch. 4th crystal is Samurai, Dragoon, CHEMIST, and dancer.
Rule 3. You can switch any character to any of the jobs you have. At least one person needs to be each job, so, after the 2nd crystal, you can have 3 of 1 job, 1 of the other, 2 and 2, or 1 and 3. 3rd crystal you will have 2 doubled up, and 1 of the other two, and the fourth crystal will have one person as each job. You can freely switch it up, and it is encouraged to, so you can find synergies between skills and abilities of the four jobs you have access to. For example, if your 1st job is black mage, and your second is red mage, it would make sense to train your final blackmage up to max level in redmage to give it xmagic, for doublecasting purposes.
Rule 4. Have fun.
The other rules are merely alternate rulesets that modify the list of rules. For example, Hard Mode puts ALL the jobs open in the pot to select from, though it will never double up, except under the berserker risk ruleset. So, for a quick example, first crystal you have the 6 jobs available, then 2nd crystal you have 10 jobs, the 5 remaining from the first crystal, and the 5 new ones. Third crystal is 13, 5 new ones, and the 7 that were left. Finally, you have the last set of jobs, 16, 4 from the final set, and 12 left selected. The reason it is hardmode is that you can very easily end up with a party of white mage, black mage, berserker, and monk, where as the normal selection assures at least a decent cross selection. Also, a VERY minimal chance of getting a chemist.