@PlayaMoon

Been a while since I used zmodeler and i dont have a current license so I cant tell you the exact steps to do this, but your issue is due to the fact that I dont think you have set up the vertex properties correctly
Its where you specify how many bones affect each vertex point, number of UV channels etc

This is part one of the video that you linked and around 2 minutes in, they go through the process I described above.

Apologies if you have already done this step and the problem is something else

Cant help too much on the former issue as thats definitely a rigging problem. When you say everything 'looks' correct with the rigging, are you sure that every vertex is correctly weighted. Did you use the brush to paint weights or did you use the fill tool on groups of vertices
If its the former, its very possible to miss vertices that are behind other vertices due to the less than ideal way in which the brush tool applies weights to vertices that are behind other ones. Had a lot of issues with this when I used to deal with shoe models

On the second point, whilst the vertex colouring tool is not very user friendly, much like the whole program its actually pretty simple once you know how to actually use it. Unfortunately it can take months to get to grips with ZM3 purely because the UI is so bad

As for a simple video of someone colouring vertexes,
try

(not my work)
minute 2:30 onwards should give you more of a pointer
And to stop the wind effect, you want to change the RGB colour of the secondary vertex colour channel to black. By default imports from other programs have the vertexes coloured white on all channels

That is a rigging issue.

From the looks of it, one of your vertices has not been assigned the correct weight to the required bone

I have had problems like this in the past, particularly with meshes that contain an outer and inner layer as it is easy to miss vertices on inner layers

This one?
https://www.gta5-mods.com/misc/realism-enhanced-traffic-and-driver-a-i

Im not an expert by any means and I only work with peds so only some may be relevant to what you are trying to do

Getting transparency to work requires 2 things

1. You need to adjust the alpha channel in the diffuse texture so that the alpha channel is less than 100%% i.e you need a level of transparaency in the diffuse texture
2. When saving the texture, if you are using compression, choose a compression model that retains the alpha channel information (DXT3, DXT5 etc). I think the alpha channel is preserved if you dont use compression
3. The shader that you assign to the material for your object HAS to support alpha channels (not all of them do)
   As an example in the ped category (ped_hair_spiked, ped_hair_cutout_alpha and ped_alpha all support alpha channels and those are the ones I have used the most

Hope that helps you get started

https://github.com/OpenIV-Team/OpenIV-PackageFormat/blob/master/specification/versions/2.1.md#file-commands

Start with this as its the most complete reference I found to the commands used for editing OIV files

I do something similar to you in my game however, to avoid having a huge assembly.xml file, I actually make the edits in the underlying meta, ymt etc files using something I knocked up in python and automatically generate the OIV
So when i then run the created installer it just move my edited files to the appropriate archives

Something like that is probably more effort than its worth for you, but my current exercise involves a lot of meshing together of lots of different mods and being able to quickly reconfigure my installed mods (and their underlying xml files) is very important to that