All skill tree for each class is under Trinity\Coroutines\AutoEquipSkills.cs
Be careful not to put in a skill lower than its level requirement, that will cause a crash
The fomulas for items are located near the end of the file Trinity\Coroutines\AutoEquipItems.cs
As far as 2h equipping, its not done well, it was much more difficult than I anticipated to evaluate 2h against 1h+shield. And this feature wasn't intended to be perfect in its evaluations since while levelling you find better items so quickly, so I wasn't particularly worried.
[Edit] it looks like I turned off 2h on Crusader due to the skill tree I picked using shield bash.