It's probably relatively easy to add a named character to a faction. I am actually going to try this with Third age Total war 3.2 later today. Here is an example
Add this and change whatever you need. This is just an example. (and make a copy of the descr_strat file first!!!!!!!!!!!!!)
character Ioannis Komnenos, named character, male, age 17, x 363, y 141
traits Supplies 1 , Turnsaway 3 , LoyaltyStarter 1 , MilitaryInclination 1 , NaturalMilitarySkill 1 , PublicFaith 1 , ReligionStarter 1
army
unit Greek Bodyguard exp 0 armour 0 weapon_lvl 0
You can take a first name from descr_names and the same sure name as the emperor. Change the age to 17, or whatever and give give him some new coordinates outside the city. Give him traits as well.
If he is the first son and heir, add this line
character Ioannis Komnenos, named character, male, age 17, x 363, y 141, battle_model byzantine_heir
Add him to the character record further down.
character_record Ioannis Komnenos, male, age 17, alive
Now you add him to the relative list underneath this
relative Manouil Komnenos, Helena Komnenos, Konstantinos Komnenos, Dimitrios Komnenos, Ioannis Komnenos, end
The firs name is the father, the second is the wife of the father, third is the first son, fourth is the second son and the fifth is the third son.
I think that is it. If there are some kind of script involved in the mod, it might be different.