At long last, I have perfected my design with a new 3D model redone from scratch, AND backed up without an armature in case i need to put it in other games!
I went from incredibly slow and annoying methods of modding and modeling, with Google Sketchup 16 and SM64 Editor, to more feature complete tools with Blender and the ability to make the custom romhack console compatible thanks to the decompilation project.
Not only that, but the latest model surpasses pretty much everything that made Mario's original model, with most notably a fully skinned body, and fully textured mesh with as few UV seams as possible.

Quick stat comparison:

Model 5
1007 triangles ( +2 for wings )
15 textures, 19456 total texels
32768 bytes of texture memory

Texels are the pixels of the textures, and both models could fit their textures on a Gameboy's screen.

Model 6
1034 triangles ( +4 for wings, + 32 for removable collar )
20 textures, 18432 total texels
26368 bytes of texture memory

These 6 models also make a great summary of the design and palette changes Martyste has gone through: when the first 3D model was completed, it was only 1 month old.

All of these screenshots have been captured with Project64 1.6 with GlideN64 3.0 graphics plugin, except the final model where PJ64 4.0 is used instead.
The last model is the only one to also include a custom model replacing Mario's Cap, its variants and when held by different entities, not shown here.