1) Is it possible to alter attack ability's so that only artillery can destroy buildings and walls?
I'm not sure about it, but I think it's in the: db_150.zip\db\Simulation\dbcomba5.csv file. However I haven't tested it much.
2) Add ability to allow units to walk through tree's? ala the old Viking and partisan unit in the original EE?
I haven't played the normal EE1 much. Unfortunately I don't know the answer for this question, but I think it's not possible. I never seen such effect in EE2 files.
3) Can you add in any moral effects that make units break and run?
With area effects you can make units faster. So you should see examples in db.zip\db\AreaEffects
4) Is there a way to add civ specific units graphics that replace the original unit graphic s without having to create a new unit for each?
I think it's somehow made in graphics files.
For example I made tricks with City Center models in epoch 15:
zips\graphics_150
Bld_citycenter15_af.nifcache
Bld_citycenter15_am.nifcache
Bld_citycenter15_fe.nifcache
Bld_citycenter15_me.nifcache
Bld_citycenter15_we.nifcache
The game is reading _af, _am, _fe, _me, _we as regions and sets the right unit models depending on the civilization. I don't know, maybe it can be the same with civilizations, but I haven't tested it.
My modding knowledge isn't very advanced, because I had not any tutorial/guide. So I was learning by watching files of the Realistic Mod (
http://ee.heavengames.com/downloads/showfile.php?fileid=2925 ). That's why I don't know everything, just the things I tested by myself.