I've been using brawlbox to slowly but surely switch out the parts, but I'll switch to brawlcrate since it seems to be more up to date. Attaching the mesh to the correct bone has been a bit of a challenge. I'll keep pounding away at it, but I'll go ahead and list the steps I've been taking.
1. To open a model in brawlcrate, launch the program then drag and drop the file into the window. In our case we're using model 255. Expand 3DModels(NW4R)
2. Highlight rtm_samus_old first, then expand it. Now expand the Objects folder
3. Right click on polygon1 and export as .obj. Do the same for polygon2.
4. Import both .obj files into blender and highlight them. Press Ctrl+J to merge them into a single file. Now export as shoulders.dae
5. Back in Brawlcrate, drag model 0 over in order to open it.
6. Right click on on the small, red BRES icon > Import > Model, and select shoulders.dae. I believe the Model Version needs to be 11, but I'm not sure
7. Expand "samus_normal" and its Objects folder and highlight polygon1. At the top, copy the vertexnode/normalnode name. Also note that it's using TextureCoordinate #1
8. In the UVs folder, delete #1. Within the Vertices folder and Normals folder, delete the files with the same name you copied
9. Now expand the "shoulders" model. We're going to rename #0 in the UVs folder to #1 and place it in the UVs folder in the "samus_normal" UVs folder directly below #0.
10. Now we'll do the same thing in the Vertices and Normals folder. Rename both to the copied text from the prior vertexnode/normalnode an place the in their corresponding location in the "samus_normal" model.
11. Finally, open the Objects folder for both models. Within the "shoulders" model, make sure the object is renamed to "replacement" or something like that. Now drag it into the "samus_normal" Objects folder.
12. Try to to make the text in the Replacement file look like the Polygon1 file. Then delete polygon1 and rename Replacment to polygon1
13. Delete the "shoulders" model. (skipping this step will cause a game crash and seems to corrupt the mesh for some reason)
14. File > Save ( You should probably make a backup first, though) (Save As results in a .brres file)
15. Repeat for every other mesh
*NOTE* This doesn't currently import the mesh properly. The mesh doesn't appear to attach to the correct bone.
Sometimes this works and will load in game. Sometimes it doesn't. The mesh may become corrupt, or the UVs may not work resulting in bad textures. Switching the order of operations doesn't seem to result in any different percentage of success rate, but YMMV. Hopefully switching from brawlbox.78 to brawlcrate.37 will help. Setting "bind" within the polygon1 notes will foprce the mesh to that particular bone, but I still haven't gotten it to work quite right.
Some adjustments can be made by right clicking on the model and selecting Preview. It allows for rotation,translation, and scaling. This whole job might be extremely easy for someone who has experience with brawlcrate, as I'm just learning it as I go.
As long as the textures from "255" are resized, they are easily imported in place of "0"s. Too many seem to crash the game though, or it may just be 1 or 2 that cause the crash. So far I've only swapped samus_arm and samus_arm_bm and it still loads.