Well I'm not the hardest core stat cruncher around but I can help with a few of these:
To restore the tactican NPCs:
In Character.txt
Change the "HardcoreNPC" entry to this:
new entry "HardcoreNPC"
type "Character"
data "Vitality" "20"
data "ChanceToHitBoost" "20"
I'm not familiar enough with Scales to know what "class focus" is, what does it do?
If it is what I think it is, it's probably in the base.charscript file.
Get yourself a copy of the base.charscript file from MAIN using the pak extractor and compare it with the one from scales.
Several entries in that file refer to the "masterclass"
THEN
CharacterConsume(__Me,MasterWaterMage,1,1)
ENDIF
I assume the leadership changes are buried in one of the scripts as well.