Good news everyone! After a lot of tinkering with the G.E.C.K, I was able to transfer her custom hair over.
First, find out what custom hair style you want on her in the G.E.C.K., using a hair mod. I used the one that comes bundled with Project Beauty. Under NPCS find Sydney, go to Headparts, and check out the various hair styles for her. Once you pick a style, look at its name, take note of it. Go to the top menus and under 'Character' will be 'Hair...'. If it gives a warning don't worry about it. Find the style you want by name, and look at the EditorID, and the Art and Texture files. It would be best to find the two files now.
For simplicity's sake, I'll refer to the 'FO3idkrrr09' style from the Saram pack (I think), it is the one used in the screenshots.
Now open up the new mod you made when you copied over Sydney's Project Beauty face. At the top menu for 'Character', go to 'Hair...' again. You'll notice that there are only the default choices here, to put the custom ones in we'll have to add them in manually. Go to the bottom of the style list and right click on the blank entry. Click new, and it will ask you to enter an EditorID. I'm not sure if you have to, but I kept the EditorID the same as it was in the other mod, so FO3idkrrr09 for this style. In the other boxes, fill in the name, again, I put FO3idkrrr09 but I think you could rename it if you wanted. Check the 'Playable' box, not sure if this is required but it worked for me. The art file is found in your Data/Meshes/Characters/hair folder, FO3idkrrr09.nif for me. The texture file is in your Data/Textures/Characters/hair folder, saram.dds for me. You should now have the new hair in the list. Keep this window open.
Now we have to add it to the 'race' we want to use it in. Go to the side menu, expand 'Actor Data', and open up 'Race'. In the main list at the top should be 1SydneyRace0. In this mod, Sydney has her own race. Double click on that, and in the new window go to the 'Face Data' menu. See the hair styles list? Now go back to the other window where we created the custom hair style, click on the custom one, and drag it into Sydney's race window's hair list. It should add the custom one to her list.
Now go find the NPC '1SydneyHairTemplate0', under her 'Head Parts' screen, in the 'Hair' drop down menu, change the style to the custom one. Save your mod, and it should work. Like before, in FOMM make sure that the original mod is loaded pretty much after everything else, and then have this mod load after that.
Sorry if this was bit long winded, but I hope this helps.
FYI, if you left Sydney at the Citadel and waited 2 weeks but keep getting the message she is still researching when trying to recall her, it's won't work that way. She is usually in the courtyard, generally target shooting with the lasers. You just need to go up to her and start a conversation to get her to go back out exploring.
In the museum of History, there are a number of items to collect and I could not find Lincoln's Repeater. I know my companions in Oblivion steal stuff in my house, take weapons from my weapon displays so when I almost gave up looking for it, I checked her inventory and there it was. So if she likes it, I let her keep it so I spawned a replica to myself with the console and also I gave her some .44 ammo and now she use it. ;)
How do I change her hairstyle to the one in the screenshots?
I installed the mod, finished the quest, and got Sydney as a follower.. but for some reason she doesn't have her SMG, and I can't remove/change her armor. Everything else about the mod works.. she follows me, listens to orders, and I can swap her weapons. Just not sure what's going on with the SMG and Armor situation.
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First, find out what custom hair style you want on her in the G.E.C.K., using a hair mod. I used the one that comes bundled with Project Beauty. Under NPCS find Sydney, go to Headparts, and check out the various hair styles for her. Once you pick a style, look at its name, take note of it. Go to the top menus and under 'Character' will be 'Hair...'. If it gives a warning don't worry about it. Find the style you want by name, and look at the EditorID, and the Art and Texture files. It would be best to find the two files now.
For simplicity's sake, I'll refer to the 'FO3idkrrr09' style from the Saram pack (I think), it is the one used in the screenshots.
Now open up the new mod you made when you copied over Sydney's Project Beauty face. At the top menu for 'Character', go to 'Hair...' again. You'll notice that there are only the default choices here, to put the custom ones in we'll have to add them in manually. Go to the bottom of the style list and right click on the blank entry. Click new, and it will ask you to enter an EditorID. I'm not sure if you have to, but I kept the EditorID the same as it was in the other mod, so FO3idkrrr09 for this style. In the other boxes, fill in the name, again, I put FO3idkrrr09 but I think you could rename it if you wanted. Check the 'Playable' box, not sure if this is required but it worked for me. The art file is found in your Data/Meshes/Characters/hair folder, FO3idkrrr09.nif for me. The texture file is in your Data/Textures/Characters/hair folder, saram.dds for me. You should now have the new hair in the list. Keep this window open.
Now we have to add it to the 'race' we want to use it in. Go to the side menu, expand 'Actor Data', and open up 'Race'. In the main list at the top should be 1SydneyRace0. In this mod, Sydney has her own race. Double click on that, and in the new window go to the 'Face Data' menu. See the hair styles list? Now go back to the other window where we created the custom hair style, click on the custom one, and drag it into Sydney's race window's hair list. It should add the custom one to her list.
Now go find the NPC '1SydneyHairTemplate0', under her 'Head Parts' screen, in the 'Hair' drop down menu, change the style to the custom one. Save your mod, and it should work. Like before, in FOMM make sure that the original mod is loaded pretty much after everything else, and then have this mod load after that.
Sorry if this was bit long winded, but I hope this helps.
How do I change her hairstyle to the one in the screenshots?
And this doesn't happen if you do installations right.
EDIT: So it turns out the "Sharing and Caring Companions" Mod was causing this. Removing it fixed the problem.