Nevermind I found a work around. Set all the costs of the spell books to 10 and then set whatever costs to the extra abilities you want to. I.E. If you wanted to set all the secondary ability costs to 2 so you can only choose 3 of them. Then set Path of XXXX to Req level 2 only level 2 you can have it that you can choose what path you want to chase down dependent upon your circumstances for each character at game start. Then set the mage books to be given as ability bonuses for taking path of the mage, and the book of life/death for path of the defender. Add whatever else you want for the rest of the paths to balance them out. You could even set it that Path of the mage / Gov. has +0 hp/ lvl, Path of Assasin +1 Hp +1 Dodge / lvl (subject to balance), Path of Defender +2 Hp / lvl, and Warrior +3 HP.
As an aside I thought of a possible way to solve the equipment scaling issue with regards to armor. Remove the armor component from gloves, boots, and hats and only make them bonus stats (Dodge, Init, Crit). Then balance all the weapons compared to this. This coupled with the ability to only wear what armor you are allowed to wear would allow for simple AI Script management. Of course this only works if the multiple rols for each member of a squad is allowed. Like a said its a side track, back to Path of the XXXX discussions.