[Blender, Crash 2/3] Baking texture + vertex colours w/ seperate UV maps, alpha

[Friedslick6]

Hey all. It's been a while, but I decided to take up a project again after abandoning the others I had planned.

I ripped a model of Crash Bandicoot riding his motorcycle from Crash Bandicoot 3, using chekwob's CrashEdit program to extract the files and warenhuis' Crash-Bandicoot-2-Modelexport tool to export the model to a .PLY file and the textures to a .TGA file. I converted the texture to a .PNG to optimise file size.
Then I imported it into Blender, linked the exported texture to the UV map, separated the model's transparent and opaque sections into different materials and applied appropriate settings for both.
(I also multiplied the size of the texture by 10 because I couldn't disable texture filtering in the Blender scene without breaking the transparency of textured polygons with vertex colours on them.)

I'm left with a great looking model, but I unfortunately I don't know how to proceed from here.
Firstly, I want to figure out the source of the unusual black squares on the model and fix that issue (notice the black spot near the end of the front wheel fender and the sides of the fork.)
Then I want to find a way to bake the Vertex Colour and UV Map channels simultaneously into one texture, if possible.

If anyone thinks they can help me with either issue, let me know. I'm happy to upload the Blender scene and additional assets if they're found necessary.

[Filler]

In blender. I think it's possible under Render > Bake > Bake vertex colours. You would need to store all the textures to fit and loop right as a single map, though.

[Friedslick6]

It's been a long time, but I have tried to do this again.

I disabled texture filtering and corrected rendering errors.
I taught myself how to map UVs in Blender, and now each vertex colour is mapped to a single 1024x1024 texture, seperated first by colour and then logically.

(It's not pretty, but it is packed for maximum island size).

I also optimised the textures sheet size and corrected the incorrectly exported textures, and corrected the UV mapping to fit over the entire of each texture.

But I've come to the conclusion that I'm still no further to my end goal since my last attempt.
At least I know exactly how to explain the problem now:

• I cannot fix the overlapping vertices in the UV map of the textures without duplicating and modifying those textures several times in the sheet.
  
• The sheet is too small for an accurate bake of the vertex colours onto the textures.
  

So my options are:

1. Bake the textures into the baked vertex colour texture (with transparency for the eyebrows)
   
2. Export the model into a format that supports two texture channels and UV sets (one for the vertex colours and one for the texture sheet), and blending between those texture channels.
   

And I don't know how to pursue either.
Whatever the case, I think including an optimised version of the PLY model in the submission would be a good idea.