Tables that modify VE use

[Widebody06]

E40 LS2-
What I'm wondering is which tables add or subtract from VE figures to account for variation is ECT and all the other factors it considers. I'm asking this from the stand point of which tables that work with VE should remain stock for most applications. And of course which tables should be modified to reflect out engine mods. I'm trying to gather info for redoing VE and MAF cal in the near future, and figure it would be smart to know which to leave stock and which to change.
Goal is to get best tune out of standard OS- std MAF/SD operation.