Edit 5: It's come to my attention that you can't use the ADD STAT effect on custom stats. How do you modify them?
Not true. You may have read the wiki entry about the ADD STAT effect not being modified by stats, perhaps. Custom stats can only really be modified by ADD STAT, CLEAR STAT or SET STAT. But you want to type the target stat's name in the NAME field, not the STAT field. The STAT field indicates a modifier to be added to the formula that produces the final output of the effect. The STAT field is non-functional for the ADD STAT/SET STAT effects.
For example:
You create a Damage effect. Min/Max are 100, no stat is used to modify the damage, NOGRAPH is false and the graph is not overridden, and so uses the Damage effect's default graph, which I think is MONSTERHEALTH. The formula is something like this (I think it's written out in the Effect Dictionary):
output graph(x/100) where x = {min:max}*(stat*stat percent/100)
output graph(x/100) = {100:100}*(1)
Note that if no stat is specified, that portion of the formula is omitted. So, we get graph(100/100) or graph(1). MONSTERHEALTH at 1 is something like 10, so this damage effect will apply 10 damage to its target before mitigation.
Now, skills like Coup de Grace use a character stat to determine damage. Coup de Grace uses Strength. So it's damage effect formula starts with these inputs:
MIN/MAX = 3; STAT=CHARACTER STRENGTH; STATPERCENT=100; NOGRAPH=true
Since NOGRAPH is true, the formula skips the step of referencing the graph array and looks like this:
output = {min:max}*(stat*statpercent/100)
output = {3:3}*(CHARACTER STRENGTH*100/100)
output = 3*CHARACTER STRENGTH
This is what you can't do with ADD STAT. You can't modify the output by a dynamic or static stat, which limits its functionality in a lot of ways that many modders wish we could have. I don't know if ADD STAT will use a graph or not. By default it has no graph.
Okay, that was a bunch of tangential information. Lemme address some of your other queries if I can.