This project was a lot of hard work and just had way too many headaches. I don't think I want to do something like this again unless I have 100% working tools. I learned a lot and I wanted to share in case others are doing their own mods.
Normal Maps
-When you bake your Normal Map make sure Green is DOWN.
-I set padding to 5 for a couple reasons. Mip maps will cause seamlines when a person zooms away from your model. By setting to 5 it should help that out. I baked at 2048x2048 and resized in Photoshop down to 1024. When you resize from 1024 sometimes seamlines will apear, padding helps that.
--Edit your Normal map now; (while it's still all blueish) don't AGB until after you've done all of your corrections and modifications/additions. Normalize after you're done and test using a custom shader in your 3D app. Once your normal is good, then "AGB" it.
-The correct order for an AGB Normal is:
--Red (X) --> Alpha
--Green (Y) --> Green
--Blue (Z) --> Blue
Red should end up empty (white)
What I did was I used an old DDS from the game and simply cut and paste each channel individually. That left the Red channel white.
Nif files
--Bones
-I learned that you can replace bones completely with bones you've customized. The problem is that the Bip01 is set to a certain position in the animation file. No matter what you do, the relation between Bip01 and Bip01 Pelvis will remain the same (including the distance). However, you can still reposition other bones (including Bip01 Pelvis), including props using your 3D apps bone features (I use 3DSmax).
-Props can be moved but are tricky, unless someone has a different method. Basically if you want to move a prop (like if you made your own), you will have to create a dummy bone relative to the position you want the prop to be at from Bip01. In other words, if you want the prop to be higher by a foot, you'll have to create a dummy that is 1 foot higher than Bip01. Then re-link the prop bone to the dummy. Link the dummy to Bip01. I recomend cloning another prop bone and renaming it to Dummy so it retains its bone data. If you don't do this and you move the pelvis or other major bone like the Spine (like I did) the Prop will not "synch" with the hand and you'll end up with it floating in the air, unless that's what you want.
-Removing Skin data from a Nif file is recomended if you are going to be replacing bones. Simply select the NiSkinInstance block of the component/model you're going to be working with and select "Remove Branch". The model will lose it's skin data. Edit/import/replace etc, the bones in question. Once that's all done, bring in your NiSkinInstance and assign it to the NiTriShape. If you don't do this, sometimes the NiSkinInstance will start spitting out all it's missing bone assignments.
-Cleaning up unused bones in your skin. Although you must have the same bones in the scene you export as the animation you'll be using (so you don't get those warnings), the 3D Skin mesh doesn't have to have those bones. I just removed them and never assigned them to the skin, they won't be loaded into memory anyways when the game loads that resource.
-NiMultiTargetTransformController; I'm not sure what this is but if you remove any bones you'll have to redeclare them here.
Minor alterations are possible, major alterations are such a pain though
The biggest hardache I had was the leg structure of the daemonette.
