In S&S I left the dragons at 240 manacost to summon, hence their strength. I guess in Singleplayer initial costs matter little however.
Aside from graphical and text mods, Ziggurat is split between the Release folder's files and the AoWEpack.dpl file.
The release folder contains among other things:
Unit stats and abilities
Recruitment lists
Spell mana/research/upkeep/sphere/tier
Dungeon defender lists (vanilla in Zigg's case)
Hero chassis base stats and abilities
Levelup availability and skillpoint cost of abilities (except multilevel abilities)
Assignation of unit graphics
You might be able to figure out which files in the folder contains which things, or maybe they're mostly all in Release.hss itself.
AoWEpack.dpl contains among other things:
Skillpoints per level (unchanged in Zigg)
Skillpoint cost of stats and multilevel abilities
base vision range and gold upkeep formula
cost of city upgrade and walls
cost of building a watchtower
installation time
ALL modifications to ATK/DAM/RANGE/RoF of spells and abilities
Scaling of the morale DEF/RES modifier and the leadership ATK/DEF modifier
XP per level requirement (scales to larger numbers at high levels)
Altar manacost/recharge time
I played a couple turns as dark elves on that map and didn't encounter the bug, and for Frostlings only this hero was bugged. It's because he is set to have +2 DEF and in Ziggurat that costs and extra 10 points. So he starts at -10, then when he levelled up it went to 0/0. I don't know how you got far more negative numbers, starting at -16, for the same hero, and then getting WORSE at levelup, weird.. Try reinstalling the mod (it has been updated a fair amount)? Is steam messing it up by verifying files?