Fleeing is an optional setting for NPCs that can be set in the npc_types table. You can enable or disable it depending on if you want the NPC to flee or not. There are a few flee settings in your rules table that can be adjusted to however you want them. Here are the defaults from the source:
Code:
RULE_INT ( Combat, FleeHPRatio, 25)
RULE_INT ( Combat, FleeSnareHPRatio, 11) // HP at which snare will halt movement of a fleeing NPC.
RULE_BOOL ( Combat, FleeIfNotAlone, false) // If false, mobs won't flee if other mobs are in combat with it.
Database settings will override the source defaults, so check your rule_values table settings and adjust as you wish.
I believe skeletons (maybe all undead) will attack you no matter what level you are. This mimics how it works on Live, unless that has been changed. On EQEmu, I think you just set the intelligence below 60 (or something) if you want a KoS NPC to attack players even if they are green/grey cons.
As far as adjusting actual combat damage/hits, that is a bit more complicated. You can adjust multiple stats in the npc_types table to get your parse results closer to Live. Most likely, it would be hard or impossible to make them match Live exactly unless you do source code edits to the combat code itself. Since we do not have the actual formulas for every factor into combat, it is nearly impossible to match Live exactly. Much of the combat code for EQEmu was created by guessing formulas that got as close to the desired results as possible within a reasonable amount of time investment.
If you can find or figure out all of the exact formulas to mimic Live content, then I am sure they can be added to the source. But, without adjustments that are huge improvements toward mimicking Live, it is generally not worth the headache it will cause all server admins as noted by jsr in the above post. The core combat system has had major adjustments to it over the years and each time it requires manually adjusting nearly all content on all servers to balance content out again. This is something that is not well received by server admins due to the huge amount of time it takes to make the adjustments.